Open access article in Journal of Synchrotron Radiation

Current events

2013-05-01

Efficient focusing of 8 keV X-rays with multilayer Fresnel zone plates fabricated by atomic layer deposition and focused ion beam milling

Mayer, M. — 2013-05-01

Fresnel zone plates (FZPs) recently showed significant improvement by focusing soft X-rays down to ∼10 nm. In contrast to soft X-rays, generally a very high aspect ratio FZP is needed for efficient focusing of hard X-rays. Therefore, FZPs had limited success in the hard X-ray range owing to difficulties of manufacturing high-aspect-ratio zone plates using conventional techniques. Here, employing a method of fabrication based on atomic layer deposition (ALD) and focused ion beam (FIB) milling, FZPs with very high aspect ratios were prepared. Such multilayer FZPs with outermost zone widths of 10 and 35 nm and aspect ratios of up to 243 were tested for their focusing properties at 8 keV and shown to focus hard X-rays efficiently. This success was enabled by the outstanding layer quality thanks to ALD. Via the use of FIB for slicing the multilayer structures, desired aspect ratios could be obtained by precisely controlling the thickness. Experimental diffraction efficiencies of multilayer FZPs fabricated via this combination reached up to 15.58% at 8 keV. In addition, scanning transmission X-ray microscopy experiments at 1.5 keV were carried out using one of the multilayer FZPs and resolved a 60 nm feature size. Finally, the prospective of different material combinations with various outermost zone widths at 8 and 17 keV is discussed in the light of the coupled wave theory and the thin-grating approximation. Al2O3/Ir is outlined as a promising future material candidate for extremely high resolution with a theoretical efficiency of more than 20% for as small an outermost zone width as 10 nm at 17 keV.

Free-electron lasers and JSR

Schlichting, I. — 2013-03-01

Current events

2013-03-01

Radiation damage to biological macromolecules: some answers and more questions

Garman, E.F. — 2013-01-01

Research into radiation damage in macromolecular crystallography has matured over the last few years, resulting in a better understanding of both the processes and timescales involved. In turn this is now allowing practical recommendations for the optimization of crystal dose lifetime to be suggested. Some long-standing questions have been answered by recent investigations, and from these answers new challenges arise and areas of investigation can be proposed. Six papers published in this volume give an indication of some of the current directions of this field and also that of single-particle cryo-microscopy, and the brief summary below places them into the overall framework of ongoing research into macromolecular crystallography radiation damage.

Enhancement in statistical and image analysis for in situ µSXRF studies of elemental distribution and co-localization, using Dioscorea balcanica

Dučić, T. — 2013-03-01

Synchrotron-based X-ray microfluorescence (µSXRF) is an analytical method suitable for in situ investigation of the distribution of micronutrient and macronutrient elements in several-micrometres-thick unstained biological samples, e.g. single cells and tissues. Elements are mapped and quantified at sub-p.p.m. concentrations. In this study the quantity, distribution and grouping/co-localization of various elements have been identified in straight and twisted internodes of the stems of the monocotyledonous climber D. balcanica Košanin. Three different statistical methods were employed to analyse the macronutrient and micronutrient distributions and co-localization. Macronutrient elements (K, P, Ca, Cl) are distributed homogeneously in both straight and twisted internodes. Micronutrient elements are mostly grouped in the vasculature and in the sclerenchyma cell layer. In addition, co-localization of micronutrient elements is much more prominent in twisted than in straight internodes. These image analyses and statistical methods provided very similar outcomes and could be applied to various types of biological samples imaged by µSXRF.

Mo/Si multilayer-coated amplitude-division beam splitters for XUV radiation sources

Sobierajski, R. — 2013-03-01

Amplitude-division beam splitters for XUV radiation sources have been developed and extensively characterized. Mo/Si multilayer coatings were deposited on 50 nm-thick SiN membranes. By changing the multilayer structure (periodicity, number of bilayers, etc.) the intensity of the reflected and transmitted beams were optimized for selected incident radiation parameters (wavelength, incident angle). The developed optical elements were characterized by means of XUV reflectometry and transmission measurements, atomic force microscopy and optical interferometry. Special attention was paid to the spatial homogeneity of the optical response and reflected beam wavefront distortions. Here the results of the characterization are presented and improvements required for advanced applications at XUV free-electron lasers are identified. A flatness as low as 4 nm r.m.s. on 3 × 3 mm beam splitters and 22 nm r.m.s. on 10 × 10 mm beam splitters has been obtained. The high-spatial-frequency surface roughness was about 0.7–1 nm r.m.s. The middle-spatial-frequency roughness was in the range 0.2–0.8 nm r.m.s. The reflection and transmission of the beam splitters were found to be very homogeneous, with a deviation of less than 2% across the full optical element.

Sagittal focusing of synchrotron radiation X-rays using a winged crystal

Nisawa, A. — 2013-03-01

A Si(111) winged crystal has been designed to minimize anticlastic bending and improve sagittal focusing efficiency. The crystal was thin with wide stiffening wings. The length-to-width ratio of the crystal was optimized by finite element analysis, and the optimal value was larger than the `golden value'. The analysis showed that the slope error owing to anticlastic bending is less than the Darwin width. The X-rays were focused two-dimensionally using the crystal and a tangentially bent mirror. The observed profiles of the focal spot agreed well with the results of a ray-tracing calculation in the energy range from 8 to 17.5 keV. X-ray diffraction measurements with a high signal-to-noise ratio using this focusing system were demonstrated for a small protein crystal.

To scavenge or not to scavenge, that is STILL the question

Allan, E.G. — 2013-01-01

An extensive radiation chemistry literature would suggest that the addition of certain radical scavengers might mitigate the effects of radiation damage during protein crystallography diffraction data collection. However, attempts to demonstrate and quantify such an amelioration and its dose dependence have not yielded consistent results, either at room temperature (RT) or 100 K. Here the information thus far available is summarized and reasons for this lack of quantitative success are identified. Firstly, several different metrics have been used to monitor and quantify the rate of damage, and, as shown here, these can give results which are in conflict regarding scavenger efficacy. In addition, significant variation in results from data collected from crystals treated in nominally the same way has been observed. Secondly, typical crystallization conditions contain substantial concentrations of chemical species which already interact strongly with some of the X-ray-induced radicals that the added scavengers are intended to intercept. These interactions are probed here by the complementary technique of on-line microspectrophotometry carried out on solutions and crystals held both at 100 K and RT, the latter enabled by the use of a beamline-mounted humidifying device. With the help of computational chemistry, attempts are made to assign some of the characteristic spectral features observed experimentally. A further source of uncertainty undoubtedly lies in the challenge of reliably measuring the parameters necessary for the accurate calculation of the absorbed dose (e.g. crystal size and shape, beam profile) and its distribution within the volume of the crystal (an issue addressed in detail in another article in this issue). While microspectrophotometry reveals that the production of various species can be quenched by the addition of scavengers, it is less clear that this observation can be translated into a significant gain in crystal dose tolerance for macromolecular crystallographers.

ANKAphase: software for single-distance phase retrieval from inline X-ray phase-contrast radiographs. Erratum

Weitkamp, T. — 2013-01-01

An equation in the paper by Weitkamp et al. [(2011), J. Synchrotron Rad. 18, 617–629] is corrected.

Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images

Karimi Nejadasl, F. — 2013-01-01

The typical dose used to record cryo-electron microscopy images from vitrified biological specimens is so high that radiation-induced structural alterations are bound to occur during data acquisition. Integration of all scattered electrons into one image can lead to significant blurring, particularly if the data are collected from an unsupported thin layer of ice suspended over the holes of a support film. Here, the dose has been fractioned and exposure series have been acquired in order to study beam-induced specimen movements under low dose conditions, prior to bubbling. Gold particles were added to the protein sample as fiducial markers. These were automatically localized and tracked throughout the exposure series and showed correlated motions within small patches, with larger amplitudes of motion vectors at the start of a series compared with the end of each series. A non-rigid scheme was used to register all images within each exposure series, using natural neighbor interpolation with the gold particles as anchor points. The procedure increases the contrast and resolution of the examined macromolecules.

International Workshop on Improving Data Quality and Quantity for XAFS Experiments (Q2XAFS 2011)

Ascone, I. — 2012-11-01

An introductory overview to the special issue papers from the Q2XAFS Workshop in this issue of the journal.

A simultaneous multiple angle-wavelength dispersive X-ray reflectometer using a bent-twisted polychromator crystal

Matsushita, T. — 2013-01-01

An X-ray reflectometer has been developed, which can simultaneously measure the whole specular X-ray reflectivity curve with no need for rotation of the sample, detector or monochromator crystal during the measurement. A bent-twisted crystal polychromator is used to realise a convergent X-ray beam which has continuously varying energy E (wavelength λ) and glancing angle α to the sample surface as a function of horizontal direction. This convergent beam is reflected in the vertical direction by the sample placed horizontally at the focus and then diverges horizontally and vertically. The normalized intensity distribution of the reflected beam measured downstream of the specimen with a two-dimensional pixel array detector (PILATUS 100K) represents the reflectivity curve. Specular X-ray reflectivity curves were measured from a commercially available silicon (100) wafer, a thin gold film coated on a silicon single-crystal substrate and the surface of liquid ethylene glycol with data collection times of 0.01 to 1000 s using synchrotron radiation from a bending-magnet source of a 6.5 GeV electron storage ring. A typical value of the simultaneously covered range of the momentum transfer was 0.01–0.45 Å−1 for the silicon wafer sample. The potential of this reflectometer for time-resolved X-ray studies of irreversible structural changes is discussed.

Current events

2012-11-01

Current events

2013-01-01

X-ray photon correlation spectroscopy using a fast pixel array detector with a grid mask resolution enhancer

Hoshino, T. — 2012-11-01

The performance of a fast pixel array detector with a grid mask resolution enhancer has been demonstrated for X-ray photon correlation spectroscopy (XPCS) measurements to investigate fast dynamics on a microscopic scale. A detecting system, in which each pixel of a single-photon-counting pixel array detector, PILATUS, is covered by grid mask apertures, was constructed for XPCS measurements of silica nanoparticles in polymer melts. The experimental results are confirmed to be consistent by comparison with other independent experiments. By applying this method, XPCS measurements can be carried out by customizing the hole size of the grid mask to suit the experimental conditions, such as beam size, detector size and sample-to-detector distance.

Towards data format standardization for X-ray absorption spectroscopy

Ravel, B. — 2012-11-01

A working group on data format standardization for X-ray absorption spectroscopy (XAS) has recently formed under the auspices of the International X-ray Absorption Society and the XAFS Commission of the International Union of Crystallography. This group of beamline scientists and XAS practitioners has been tasked to propose data format standards to meet the needs of the world-wide XAS community. In this report, concepts for addressing three XAS data storage needs are presented: a single spectrum interchange format, a hierarchical format for multispectral X-ray experiment, and a relational database format for XAS data libraries.

A hard X-ray nanoprobe beamline for nanoscale microscopy

Winarski, R.P. — 2012-11-01

The Hard X-ray Nanoprobe Beamline (or Nanoprobe Beamline) is an X-ray microscopy facility incorporating diffraction, fluorescence and full-field imaging capabilities designed and operated by the Center for Nanoscale Materials and the Advanced Photon Source at Sector 26 of the Advanced Photon Source at Argonne National Laboratory. This facility was constructed to probe the nanoscale structure of biological, environmental and material sciences samples. The beamline provides intense focused X-rays to the Hard X-ray Nanoprobe (or Nanoprobe) which incorporates Fresnel zone plate optics and a precision laser sensing and control system. The beamline operates over X-ray energies from 3 to 30 keV, enabling studies of most elements in the periodic table, with a particular emphasis on imaging transition metals.

Capturing dynamics with Eiger, a fast-framing X-ray detector

Johnson, I. — 2012-11-01

Eiger is the next-generation single-photon-counting pixel detector following the widely used Pilatus detector. Its smaller pixel size of 75 µm × 75 µm, higher frame rate of up to 22 kHz, and practically zero dead-time (∼4 µs) between exposures will further various measurement methods at synchrotron sources. In this article Eiger's suitability for X-ray photon correlation spectroscopy (XPCS) is demonstrated. By exploiting its high frame rate, complementary small-angle X-ray scattering (SAXS) and XPCS data are collected in parallel to determine both the structure factor and collective diffusion coefficient of a nano-colloid suspension. For the first time, correlation times on the submillisecond time scale are accessible with a large-area pixel detector.

The point-spread function of fiber-coupled area detectors

Holton, J.M. — 2012-11-01

The point-spread function (PSF) of a fiber-optic taper-coupled CCD area detector was measured over five decades of intensity using a 20 µm X-ray beam and ∼2000-fold averaging. The `tails' of the PSF clearly revealed that it is neither Gaussian nor Lorentzian, but instead resembles the solid angle subtended by a pixel at a point source of light held a small distance (∼27 µm) above the pixel plane. This converges to an inverse cube law far from the beam impact point. Further analysis revealed that the tails are dominated by the fiber-optic taper, with negligible contribution from the phosphor, suggesting that the PSF of all fiber-coupled CCD-type detectors is best described as a Moffat function.

Current events

2012-09-01

Regridding reconstruction algorithm for real-time tomographic imaging

Marone, F. — 2012-11-01

Sub-second temporal-resolution tomographic microscopy is becoming a reality at third-generation synchrotron sources. Efficient data handling and post-processing is, however, difficult when the data rates are close to 10 GB s−1. This bottleneck still hinders exploitation of the full potential inherent in the ultrafast acquisition speed. In this paper the fast reconstruction algorithm gridrec, highly optimized for conventional CPU technology, is presented. It is shown that gridrec is a valuable alternative to standard filtered back-projection routines, despite being based on the Fourier transform method. In fact, the regridding procedure used for resampling the Fourier space from polar to Cartesian coordinates couples excellent performance with negligible accuracy degradation. The stronger dependence of the observed signal-to-noise ratio for gridrec reconstructions on the number of angular views makes the presented algorithm even superior to filtered back-projection when the tomographic problem is well sampled. Gridrec not only guarantees high-quality results but it provides up to 20-fold performance increase, making real-time monitoring of the sub-second acquisition process a reality.

The new ambient-pressure X-ray photoelectron spectroscopy instrument at MAX-lab

Schnadt, J. — 2012-09-01

The new instrument for near-ambient-pressure X-ray photoelectron spectroscopy which has been installed at the MAX II ring of the Swedish synchrotron radiation facility MAX IV Laboratory in Lund is presented. The new instrument, which is based on a SPECS PHOIBOS 150 NAP analyser, is the first to feature the use of retractable and exchangeable high-pressure cells. This implies that clean vacuum conditions are retained in the instrument's analysis chamber and that it is possible to swiftly change between near-ambient and ultrahigh-vacuum conditions. In this way the instrument implements a direct link between ultrahigh-vacuum and in situ studies, and the entire pressure range from ultrahigh-vacuum to near-ambient conditions is available to the user. Measurements at pressures up to 10−5 mbar are carried out in the ultrahigh-vacuum analysis chamber, while measurements at higher pressures are performed in the high-pressure cell. The installation of a mass spectrometer on the exhaust line of the reaction cell offers the users the additional dimension of simultaneous reaction data monitoring. Moreover, the chosen design approach allows the use of dedicated cells for different sample environments, rendering the Swedish ambient-pressure X-ray photoelectron spectroscopy instrument a highly versatile and flexible tool.

Exploration of synchrotron Mössbauer microscopy with micrometer resolution: forward and a new backscattering modality on natural samples

Yan, L. — 2012-09-01

New aspects of synchrotron Mössbauer microscopy are presented. A 5 µm spatial resolution is achieved, and sub-micrometer resolution is envisioned. Two distinct and unique methods, synchrotron Mössbauer imaging and nuclear resonant incoherent X-ray imaging, are used to resolve spatial distribution of species that are chemically and magnetically distinct from one another. Proof-of-principle experiments were performed on enriched 57Fe phantoms, and on samples with natural isotopic abundance, such as meteorites.

Zone-doubled Fresnel zone plates for high-resolution hard X-ray full-field transmission microscopy

Vila-Comamala, J. — 2012-09-01

Full-field transmission X-ray microscopy is a unique non-destructive technique for three-dimensional imaging of specimens at the nanometer scale. Here, the use of zone-doubled Fresnel zone plates to achieve a spatial resolution better than 20 nm in the hard X-ray regime (8–10 keV) is reported. By obtaining a tomographic reconstruction of a Ni/YSZ solid-oxide fuel cell, the feasibility of performing three-dimensional imaging of scientifically relevant samples using such high-spatial-resolution Fresnel zone plates is demonstrated.

Current events

2012-07-01

Glitch-free X-ray absorption spectrum under high pressure obtained using nano-polycrystalline diamond anvils

Ishimatsu, N. — 2012-09-01

Nano-polycrystalline diamond (NPD) [Irifune et al. (2003), Nature (London), 421, 599] has been used to obtain a glitch-free X-ray absorption spectrum under high pressure. In the case of conventional single-crystal diamond (SCD) anvils, glitches owing to Bragg diffraction from the anvils are superimposed on X-ray absorption spectra. The glitch has long been a serious problem for high-pressure research activities using X-ray spectroscopy because of the difficulties of its complete removal. It is demonstrated that NPD is one of the best candidate materials to overcome this problem. Here a glitch-free absorption spectrum using the NPD anvils over a wide energy range is shown. The advantage and capability of NPD anvils is discussed by a comparison of the glitch map with that of SCD anvils.

High-energy-resolution X-ray monochromator calibration using the detailed-balance principle

Zhao, J.Y. — 2012-07-01

A new method is presented to calibrate an X-ray energy scale with sub-meV relative accuracy by using the detailed-balance principle of the phonon creation and annihilation. This method is conveniently used to define or verify the energy scale of high-energy-resolution monochromators that are used in inelastic X-ray scattering and nuclear resonant inelastic X-ray scattering instruments at synchrotron radiation facilities. This method does not rely on sample properties and its precision only depends on the statistical data quality. Well calibrated instruments are essential for reliable comparison of data sets obtained at different synchrotron radiation beamlines, of data with theoretical predictions, and of data from other techniques such as neutron or light scattering. The principle of the detailed-balance method is described in this paper and demonstrated experimentally.

An X-ray diffraction study on a single rod outer segment from frog retina

Yagi, N. — 2012-07-01

X-ray diffraction patterns were recorded from isolated single rod outer segments of frog. The outer segments in Ringer's solution were exposed to a 6 µm microbeam (15 keV) at the BL40XU beamline, SPring-8. The diffraction pattern demonstrated a remarkable regularity in the stacking and flatness of the disk membranes. The electron density profile calculated from the intensity of up to tenth-order reflections showed a pair of bilayers that comprise a disk membrane. The structure of the disk membrane and the changes in the profile on swelling generally agreed with previous reports. Radiation damage was significant with an irradiation of 5 × 105 Gy which is much lower than the known damaging dose on proteins at the liquid-nitrogen temperature.

Local structural studies of the cubic Cd1–xCaxO system through Cd K-edge extended X-ray absorption spectroscopic studies

Srihari, V. — 2012-07-01

Cd K-edge extended X-ray absorption fine-structure spectroscopic studies were carried out on Cd1–xCaxO (0 ≤ x ≤0.9) solid solutions and the first and second nearest neighbour (NN) distances and their mean square relative displacement σ2 were estimated. The first NN distance, dCd–O(x), was found to be smaller than its expected value, a(x)/2, obtained from the X-ray diffraction measurements. It increases monotonically and non-linearly with a negative curvature, comparable with that of the a(x) value variation. The variation σ2 of the 1NN with x is consistent with a disordered solid solution model. The 2NN distances dCd–Cd(x) and dCd–Ca(x) are found to follow the average values obtained by X-ray diffraction with dCd–Ca(x) > dCd–Cd(x). From detailed analysis it is argued that the solid solution exhibits a bimodal distribution of the 1NN distances, dCd–O(x) and dCa–O(x), and that the system belongs to a persistent type.

P03, the microfocus and nanofocus X-ray scattering (MiNaXS) beamline of the PETRA III storage ring: the microfocus endstation

Buffet, A. — 2012-07-01

The P03 beamline, also called the microfocus and nanofocus X-ray scattering (MiNaXS) beamline, exploits the excellent photon beam properties of the low-emittance source PETRA III to provide a microfocused/nanofocused beam with ultra-high intensity for time-resolved X-ray scattering experiments. The beamline has been designed to perform X-ray scattering in both transmission and reflection geometries. The microfocus endstation started user operation in May 2011. An overview of the beamline status and of some representative results highlighting the performance of the microfocus endstation at MiNaXS are given.

The 7BM beamline at the APS: a facility for time-resolved fluid dynamics measurements

Kastengren, A. — 2012-07-01

In recent years, X-ray radiography has been used to probe the internal structure of dense sprays with microsecond time resolution and a spatial resolution of 15 µm even in high-pressure environments. Recently, the 7BM beamline at the Advanced Photon Source (APS) has been commissioned to focus on the needs of X-ray spray radiography measurements. The spatial resolution and X-ray intensity at this beamline represent a significant improvement over previous time-resolved X-ray radiography measurements at the APS.

Current events

2012-05-01

Adapting federated cyberinfrastructure for shared data collection facilities in structural biology

Stokes-Rees, I. — 2012-05-01

Early stage experimental data in structural biology is generally unmaintained and inaccessible to the public. It is increasingly believed that this data, which forms the basis for each macromolecular structure discovered by this field, must be archived and, in due course, published. Furthermore, the widespread use of shared scientific facilities such as synchrotron beamlines complicates the issue of data storage, access and movement, as does the increase of remote users. This work describes a prototype system that adapts existing federated cyberinfrastructure technology and techniques to significantly improve the operational environment for users and administrators of synchrotron data collection facilities used in structural biology. This is achieved through software from the Virtual Data Toolkit and Globus, bringing together federated users and facilities from the Stanford Synchrotron Radiation Lightsource, the Advanced Photon Source, the Open Science Grid, the SBGrid Consortium and Harvard Medical School. The performance and experience with the prototype provide a model for data management at shared scientific facilities.

Performance upgrade in the JAEA actinide science beamline BL23SU at SPring-8 with a new twin-helical undulator

Saitoh, Y. — 2012-05-01

The soft X-ray beamline BL23SU at SPring-8 has undergone an upgrade with a twin-helical undulator of in-vacuum type to enhance the experimental capabilities of the endstations. The new light source with a fast helicity-switching operation allows not only the data throughput but also the sensitivity in X-ray magnetic circular dichroism (XMCD) to be improved. The operational performance and potential are described by presenting XMCD results of paramagnetic β-US2 measured with a 10 T superconducting magnet.

Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin

Mueller, U. — 2012-05-01

Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-β section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5–16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-κ goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given.

Evaluating the peak-to-valley dose ratio of synchrotron microbeams using PRESAGE fluorescence

Annabell, N. — 2012-05-01

Synchrotron-generated microbeam radiotherapy holds great promise for future treatment, but the high dose gradients present conventional dosimetry with a challenge. Measuring the important peak-to-valley dose ratio (PVDR) of a microbeam-collimated synchrotron source requires both a dosimeter and an analysis method capable of exceptional spatial resolution. The PVDR is of great interest since it is the limiting factor for potential application of the microbeam radiation therapy technique clinically for its tissue-sparing properties (i.e. the valley dose should be below the tolerance of normal tissue). In this work a new method of measuring the dose response of PRESAGE dosimeters is introduced using the fluorescence from a 638 nm laser on a confocal laser-scanning microscope. This fluorescent microscopy method produces dosimetry data at a pixel size as low as 78 nm, giving a much better spatial resolution than optical computed tomography, which is normally used for scanning PRESAGE dosimeters. Using this technique the PVDR of the BL28B2 microbeam at the SPring-8 synchrotron in Japan is estimated to be approximately 52:1 at a depth of 2.5 mm. The PVDR was also estimated with EBT2 GAFchromic films as 30.5:1 at the surface in order to compare the PRESAGE fluorescent results with a more established dosimetry system. This estimation is in good agreement with previously measured ratios using other dosimeters and Monte Carlo simulations. This means that it is possible to use PRESAGE dosimeters with confocal microscopy for the determination of PVDR.

Improved count rate corrections for highest data quality with PILATUS detectors

Trueb, P. — 2012-05-01

The PILATUS detector system is widely used for X-ray experiments at third-generation synchrotrons. It is based on a hybrid technology combining a pixelated silicon sensor with a CMOS readout chip. Its single-photon-counting capability ensures precise and noise-free measurements. The counting mechanism introduces a short dead-time after each hit, which becomes significant for rates above 106 photons s−1 pixel−1. The resulting loss in the number of counted photons is corrected for by applying corresponding rate correction factors. This article presents the results of a Monte Carlo simulation which computes the correction factors taking into account the detector settings as well as the time structure of the X-ray beam at the synchrotron. The results of the simulation show good agreement with experimentally determined correction factors for various detector settings at different synchrotrons. The application of accurate rate correction factors improves the X-ray data quality acquired at high photon fluxes. Furthermore, it is shown that the use of fast detector settings in combination with an optimized time structure of the X-ray beam allows for measurements up to rates of 107 photons s−1 pixel−1.

Development of a laser-based heating system for in situ synchrotron-based X-ray tomographic microscopy

Fife, J.L. — 2012-05-01

Understanding the formation of materials at elevated temperatures is critical for determining their final properties. Synchrotron-based X-ray tomographic microscopy is an ideal technique for studying such processes because high spatial and temporal resolutions are easily achieved and the technique is non-destructive, meaning additional analyses can take place after data collection. To exploit the state-of-the-art capabilities at the tomographic microscopy and coherent radiology experiments (TOMCAT) beamline of the Swiss Light Source, a general-use moderate-to-high-temperature furnace has been developed. Powered by two diode lasers, it provides controlled localized heating, from 673 to 1973 K, to examine many materials systems and their dynamics in real time. The system can also be operated in various thermal modalities. For example, near-isothermal conditions at a given sample location can be achieved with a prescribed time-dependent temperature. This mode is typically used to study isothermal phase transformations; for example, the formation of equiaxed grains in metallic systems or to nucleate and grow bubble foams in silicate melts under conditions that simulate volcanic processes. In another mode, the power of the laser can be fixed and the specimen moved at a constant speed in a user-defined thermal gradient. This is similar to Bridgman solidification, where the thermal gradient and cooling rate control the microstructure formation. This paper details the experimental set-up and provides multiple proofs-of-concept that illustrate the versatility of using this laser-based heating system to explore, in situ, many elevated-temperature phenomena in a variety of materials.

Micrometre resolution of a charge integrating microstrip detector with single photon sensitivity

Schubert, A. — 2012-05-01

A synchrotron beam has been used to test the spatial resolution of a single-photon-resolving integrating readout-chip coupled to a 320 µm-thick silicon strip sensor with a dedicated readout system. Charge interpolation methods have yielded a spatial resolution of σx ≃ 1.8 µm for a 20 µm-pitch strip.

Real sample temperature: a critical issue in the experiments of nuclear resonant vibrational spectroscopy on biological samples

Wang, H. — 2012-03-01

There are several practical and intertangled issues which make the experiments of nuclear resonant vibrational spectroscopy (NRVS) on biological samples difficult to perform. The sample temperature is one of the most important issues. In NRVS the real sample temperatures can be very different from the readings on the temperature sensors. In this study the following have been performed: (i) citing and analyzing various existing NRVS data to assess the real sample temperatures during the NRVS measurements and to understand their trends with the samples' loading conditions; (ii) designing several NRVS measurements with (Et4N)[FeCl4] to verify these trends; and (iii) proposing a new sample-loading procedure to achieve significantly lower real sample temperatures and to balance among the intertangled experimental issues in biological NRVS measurements.

The kinetic dose limit in room-temperature time-resolved macromolecular crystallography

Schmidt, M. — 2012-03-01

Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.

MFM and PEEM observation of micrometre-sized magnetic dot arrays fabricated by ion-microbeam irradiation in FeRh thin films

Aikoh, K. — 2012-03-01

FeRh thin films were irradiated with a 10 MeV iodine ion microbeam to produce micrometre-scale ferromagnetic microstructures by modifying the local magnetic character from antiferromagnetism to ferromagnetism using ion-microbeam irradiation. Two-dimensional magnetic dot arrays of dimensions ∼2 µm × 4 µm as well as 10 µm × 10 µm were successfully produced on the FeRh surface, which was confirmed by magnetic force microscopy (MFM). The results of photoemission electron microscopy (PEEM) combined with X-ray magnetic circular dichroism reveal that the easy axis of the magnetization of the ion-beam-irradiated ferromagnetism in the FeRh thin films lies in the film planes along the 〈001〉 direction of the MgO substrates.

On the calculation of the gauge volume size for energy-dispersive X-ray diffraction. Erratum

Rowles, M.R. — 2012-01-01

An equation in the paper by Rowles [(2011), J. Synchrotron Rad. 18, 938–941] is corrected.

Current events

2012-03-01

Current events

2012-01-01

Sub-10 nm beam confinement by X-ray waveguides: design, fabrication and characterization of optical properties

Krüger, S.P. — 2012-03-01

The propagation of hard X-ray synchrotron beams in waveguides with guiding layer diameters in the 9–35 nm thickness range has been studied. The planar waveguide structures consist of an optimized two-component cladding. The presented fabrication method is suitable for short and leak-proof waveguide slices with lengths (along the optical axis) in the sub-500 µm range, adapted for optimized transmission at photon energies of 11.5–18 keV. A detailed comparison between finite-difference simulations of waveguide optics and the experimental results is presented, concerning transmission, divergence of the waveguide exit beam, as well as the angular acceptance. In a second step, two crossed waveguides have been used to create a quasi-point source for propagation-based X-ray imaging at the new nano-focus endstation of the P10 coherence beamline at Petra III. By inverting the measured Fraunhofer diffraction pattern by an iterative error-reduction algorithm, a two-dimensional focus of 10 nm × 10 nm is obtained. Finally, holographic imaging of a lithographic test structure based on this optical system is demonstrated.

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

Liu, Y. — 2012-03-01

Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available.

Moiré pattern from a multiple Bragg–Laue interferometer

Hirano, K. — 2012-01-01

In X-ray section topography of Si 220 diffraction in a multiple Bragg–Laue mode, a moiré pattern is observed when the incident beam is divided into two parts by inserting a platinum wire in the middle of the beam. The moiré pattern can be explained by the summation of two interference fringes corresponding to the two incident beams. The coherency of the X-rays from the bending-magnet beamline is estimated using the moiré pattern.

Automatic XAFS measurement system developed at BL14B2 in SPring-8

Oji, H. — 2012-01-01

A novel XAFS measurement system has been developed in which XAFS measurements can be performed including sample-loading and detector adjustments. With this system, XAFS measurements of up to 80 samples in both transmission and fluorescence modes can be carried out. The adjustment of the optical components has also been automated. It not only saves manpower and measurement time, but also improves the accuracy and reliability of sample alignments.

Two-dimensional approach to fluorescence yield XANES measurement using a silicon drift detector. Erratum

Tamenori, Y. — 2011-11-01

An error in the paper by Tamenori et al. [(2011), J. Synchrotron Rad. 18, 747–752] is corrected.

Current events

2011-11-01

Assessing noise sources at synchrotron infrared ports

Lerch, P. — 2012-01-01

Today, the vast majority of electron storage rings delivering synchrotron radiation for general user operation offer a dedicated infrared port. There is growing interest expressed by various scientific communities to exploit the mid-IR emission in microspectroscopy, as well as the far infrared (also called THz) range for spectroscopy. Compared with a thermal (laboratory-based source), IR synchrotron radiation sources offer enhanced brilliance of about two to three orders of magnitude in the mid-IR energy range, and enhanced flux and brilliance in the far-IR energy range. Synchrotron radiation also has a unique combination of a broad wavelength band together with a well defined time structure. Thermal sources (globar, mercury filament) have excellent stability. Because the sampling rate of a typical IR Fourier-transform spectroscopy experiment is in the kHz range (depending on the bandwidth of the detector), instabilities of various origins present in synchrotron radiation sources play a crucial role. Noise recordings at two different IR ports located at the Swiss Light Source and SOLEIL (France), under conditions relevant to real experiments, are discussed. The lowest electron beam fluctuations detectable in IR spectra have been quantified and are shown to be much smaller than what is routinely recorded by beam-position monitors.

X-ray near-field speckle: implementation and critical analysis

Lu, X. — 2011-11-01

The newly introduced coherence-based technique of X-ray near-field speckle (XNFS) has been implemented at 8-ID-I at the Advanced Photon Source. In the near-field regime of high-brilliance synchrotron X-rays scattered from a sample of interest, it turns out that, when the scattered radiation and the main beam both impinge upon an X-ray area detector, the measured intensity shows low-contrast speckles, resulting from interference between the incident and scattered beams. A micrometer-resolution XNFS detector with a high numerical aperture microscope objective has been built and its capability for studying static structures and dynamics at longer length scales than traditional far-field X-ray scattering techniques is demonstrated. Specifically, the dynamics of dilute silica and polystyrene colloidal samples are characterized. This study reveals certain limitations of the XNFS technique, especially in the characterization of static structures, which is discussed.

Development of a soft X-ray angle-resolved photoemission system applicable to 100 µm crystals

Muro, T. — 2011-11-01

A system for angle-resolved photoemission spectroscopy (ARPES) of small single crystals with sizes down to 100 µm has been developed. Soft X-ray synchrotron radiation with a spot size of ∼40 µm × 65 µm at the sample position is used for the excitation. Using this system an ARPES measurement has been performed on a Si crystal of size 120 µm × 100 µm × 80 µm. The crystal was properly oriented on a sample stage by measuring the Laue spots. The crystal was cleaved in situ with a microcleaver at 100 K. The cleaved surface was adjusted to the beam spot using an optical microscope. Consequently, clear band dispersions along the Γ–X direction reflecting the bulk electronic states were observed with a photon energy of 879 eV.

Time-over-threshold readout to enhance the high flux capabilities of single-photon-counting detectors

Bergamaschi, A. — 2011-11-01

The MYTHEN single-photon-counting (SPC) detector has been characterized using the time-over-threshold (ToT) readout method, i.e. measuring the time that the signal produced by the detected X-rays remains above the comparator threshold. In the following it is shown that the ToT readout preserves the sensitivity, dynamic range and capability of background suppression of the SPC mode, while enhancing the count-rate capability, which is the main limitation of state-of-the-art SPC systems.

Current events

2011-09-01

In situ two-dimensional imaging quick-scanning XAFS with pixel array detector

Tanida, H. — 2011-11-01

Quick-scanning X-ray absorption fine structure (XAFS) measurements were performed in transmission mode using a PILATUS 100K pixel array detector (PAD). The method can display a two-dimensional image for a large area of the order of a centimetre with a spatial resolution of 0.2 mm at each energy point in the XAFS spectrum. The time resolution of the quick-scanning method ranged from 10 s to 1 min per spectrum depending on the energy range. The PAD has a wide dynamic range and low noise, so the obtained spectra have a good signal-to-noise ratio.

Fluorescence detection of white-beam X-ray absorption anisotropy: towards element-sensitive projections of local atomic structure

Korecki, P. — 2011-11-01

Projections of the atomic structure around Nb atoms in a LiNbO3 single crystal were obtained from a white-beam X-ray absorption anisotropy (XAA) pattern detected using Nb K fluorescence. This kind of anisotropy results from the interference of X-rays inside a sample and, owing to the short coherence length of a white beam, is visible only at small angles around interatomic directions. Consequently, the main features of the recorded XAA corresponded to distorted real-space projections of dense-packed atomic planes and atomic rows. A quantitative analysis of XAA was carried out using a wavelet transform and allowed well resolved projections of Nb atoms to be obtained up to distances of 10 Å. The signal of nearest O atoms was detected indirectly by a comparison with model calculations. The measurement of white-beam XAA using characteristic radiation indicates the possibility of obtaining element-sensitive projections of the local atomic structure in more complex samples.

Two-dimensional approach to fluorescence yield XANES measurement using a silicon drift detector

Tamenori, Y. — 2011-09-01

The objective of this article is to describe the capability of a two-dimensional (2D) approach to X-ray absorption near-edge structure (XANES) measurement by means of a partial fluorescence yield (PFY) method. 2D-XANES measurements were achieved by using a silicon drift detector as an energy-dispersive fluorescence detector. The advantage of this technique is that it allows full surveys of X-ray fluorescence data that are lost in conventional PFY measurements. The availability of a map approach was demonstrated by applying it to XANES measurements in both a diluted (Mn-doped nano-diamond) and a concentrated (MnO crystal) manganese sample. The 2D approach clearly distinguished between the PFY spectra of Mn and O atoms, where absorption edges of both elements are close to each other. Further, the 2D approach extracted an unambiguous PFY spectrum of phosphorus in the XANES measurement of SS304 (P < 0.045 wt%).

SHADOW3: a new version of the synchrotron X-ray optics modelling package

Sanchez del Rio, M. — 2011-09-01

A new version of the popular X-ray tracing code SHADOW is presented. An important step has been made in restructuring the code following new computer engineering standards, ending with a modular Fortran 2003 structure and an application programming interface (API). The new code has been designed to be compatible with the original file-oriented SHADOW philosophy, but simplifying the compilation, installation and use. In addition, users can now become programmers using the newly designed SHADOW3 API for creating scripts, macros and programs; being able to deal with optical system optimization, image simulation, and also low transmission calculations requiring a large number of rays (>106). Plans for future development and questions on how to accomplish them are also discussed.

Milli-electronvolt monochromatization of hard X-rays with a sapphire backscattering monochromator

Sergueev, I. — 2011-09-01

A sapphire backscattering monochromator with 1.1 (1) meV bandwidth for hard X-rays (20–40 keV) is reported. The optical quality of several sapphire crystals has been studied and the best crystal was chosen to work as the monochromator. The small energy bandwidth has been obtained by decreasing the crystal volume impinged upon by the beam and by choosing the crystal part with the best quality. The monochromator was tested at the energies of the nuclear resonances of 121Sb at 37.13 keV, 125Te at 35.49 keV, 119Sn at 23.88 keV, 149Sm at 22.50 keV and 151Eu at 21.54 keV. For each energy, specific reflections with sapphire temperatures in the 150–300 K region were chosen. Applications to nuclear inelastic scattering with these isotopes are demonstrated.

Introduction to XAFS. A Practical Guide to X-ray Absorption Fine Structure Spectroscopy. By Grant Bunker. Pp. viii + 260. Cambridge University Press, 2010. Price (hardback) GBP 40. ISBN-13: 978-0-521-76775-0.

Paufler, P. — 2011-09-01

Current events

2011-07-01

Six-reflection meV-monochromator for synchrotron radiation

Toellner, T.S. — 2011-07-01

An in-line monochromatization scheme suitable for 10–40 keV synchrotron radiation is presented based on the use of six crystal reflections that achieves meV and sub-meV bandwidths with high efficiency. The theoretical spectral efficiency surpasses all previous multicrystal designs and approaches that of single room-temperature back-reflecting crystals. This article presents the designs of two such devices along with their theoretical and measured performances.

Development of an X-ray real-time stereo imaging technique using synchrotron radiation

Hoshino, M. — 2011-07-01

An X-ray stereo imaging system with synchrotron radiation was developed at BL20B2, SPring-8. A portion of a wide X-ray beam was Bragg-reflected by a silicon crystal to produce an X-ray beam which intersects with the direct X-ray beam. Samples were placed at the intersection point of the two beam paths. X-ray stereo images were recorded simultaneously by a detector with a large field of view placed close to the sample. A three-dimensional wire-frame model of a sample was created from the depth information that was obtained from the lateral positions in the stereo image. X-ray stereo angiography of a mouse femoral region was performed as a demonstration of real-time stereo imaging. Three-dimensional arrangements of the femur and blood vessels were obtained.

Calcifications in human osteoarthritic articular cartilage: ex vivo assessment of calcium compounds using XANES spectroscopy. Addendum

Nguyen, C. — 2011-07-01

An acknowledgment is published for the paper by Nguyen et al. [(2011), J. Synchrotron Rad. 18, 475–480].

Radiation-induced melting in coherent X-ray diffractive imaging at the nanoscale

Ponomarenko, O. — 2011-07-01

Coherent X-ray diffraction techniques play an increasingly significant role in the imaging of nanoscale structures, ranging from metallic and semiconductor to biological objects. In material science, X-rays are usually considered to be of a low-destructive nature, but under certain conditions they can cause significant radiation damage and heat loading on the samples. The qualitative literature data concerning the tolerance of nanostructured samples to synchrotron radiation in coherent diffraction imaging experiments are scarce. In this work the experimental evidence of a complete destruction of polymer and gold nanosamples by the synchrotron beam is reported in the case of imaging at 1–10 nm spatial resolution. Numerical simulations based on a heat-transfer model demonstrate the high sensitivity of temperature distribution in samples to macroscopic experimental parameters such as the conduction properties of materials, radiation heat transfer and convection. However, for realistic experimental conditions the calculated rates of temperature rise alone cannot explain the melting transitions observed in the nanosamples. Comparison of these results with the literature data allows a specific scenario of the sample destruction in each particular case to be presented, and a strategy for damage reduction to be proposed.

Macromolecular crystallography radiation damage research: what's new?

Garman, E.F. — 2011-05-01

Radiation damage in macromolecular crystallography has become a mainstream concern over the last ten years. The current status of research into this area is briefly assessed, and the ten new papers published in this issue are set into the context of previous work in the field. Some novel and exciting developments emerging over the last two years are also summarized.

Current events

2011-05-01

Automatic loop centring with a high-precision goniometer head at the SLS macromolecular crystallography beamlines

Pauluhn, A. — 2011-07-01

Automatic loop centring has been developed as part of the automation process in crystallographic data collection at the Swiss Light Source. The procedure described here consists of an optional set-up part, in which the background images are taken, and the actual centring part. The algorithm uses boundary and centre-of-mass detection at two different microscope image magnifications. Micromounts can be handled as well. Centring of the loops can be achieved in 15–26 s, depending on their initial position, and as fast as manual centring. The alignment of the sample is carried out by means of a new flexural-hinge-based compact goniometer head. The device features an electromagnet for robotic wet mounting of samples. The circle of confusion was measured to be smaller than 1 µm (r.m.s.); its bidirectional backlash is below 2 µm.

DNA damage and repair kinetics after microbeam radiation therapy emulation in living cells using monoenergetic synchrotron X-ray microbeams

Sprung, C.N. — 2011-07-01

A novel synchrotron-based approach, known as microbeam radiation therapy (MRT), currently shows considerable promise in increased tumour control and reduced normal tissue damage compared with conventional radiotherapy. Different microbeam widths and separations were investigated using a controlled cell culture system and monoenergetic (5.35 keV) synchrotron X-rays in order to gain further insight into the underlying cellular response to MRT. DNA damage and repair was measured using fluorescent antibodies against phosphorylated histone H2AX, which also allowed us to verify the exact location of the microbeam path. Beam dimensions that reproduced promising MRT strategies were used to identify useful methods to study the underpinnings of MRT. These studies include the investigation of different spatial configurations on bystander effects. γH2AX foci number were robustly induced in directly hit cells and considerable DNA double-strand break repair occurred by 12 h post-10 Gy irradiation; however, many cells had some γH2AX foci at the 12 h time point. γH2AX foci at later time points did not directly correspond with the targeted regions suggesting cell movement or bystander effects as a potential mechanism for MRT effectiveness. Partial irradiation of single nuclei was also investigated and in most cases γH2AX foci were not observed outside the field of irradiation within 1 h after irradiation indicating very little chromatin movement in this time frame. These studies contribute to the understanding of the fundamental radiation biology relating to the MRT response, a potential new therapy for cancer patients.

A narrow microbeam is more effective for tumor growth suppression than a wide microbeam: an in vivo study using implanted human glioma cells

Uyama, A. — 2011-07-01

The tumoricidal mechanisms of microbeam radiation therapy, and the more recently proposed minibeam radiation therapy, for the treatment of brain tumors are as yet unclear. Moreover, from among the various parameters of beam geometry the impact of changing the beam width is unknown. In this study, suppression of tumor growth in human glioma cells implanted in mice was evaluated experimentally using microbeams of two different widths: a conventional narrow beam (20 µm width, 100 µm center-to-center distance) and a wide beam (100 µm width, 500 µm center-to-center distance). The tumor growth ratio was compared and acute cell death was studied histologically. With cross-planar irradiation, tumor growth was significantly suppressed between days 4 and 28 after 20 µm microbeam irradiation, whereas tumor growth was suppressed, and not significantly so, only between days 4 and 18 after 100 µm microbeam irradiation. Immunohistochemistry using TUNEL staining showed no increase in TUNEL-positive cells with either microbeam at 24 and 72 h post-irradiation. The 20 µm microbeam was found to be more tumoricidal than the 100 µm microbeam, and the effect was not related to apoptotic cell death. The underlying mechanism may be functional tissue deterioration rather than direct cellular damage in the beam path.

Achromatic nested Kirkpatrick–Baez mirror optics for hard X-ray nanofocusing

Liu, W. — 2011-07-01

The first test of nanoscale-focusing Kirkpatrick–Baez (KB) mirrors in the nested (or Montel) configuration used at a hard X-ray synchrotron beamline is reported. The two mirrors are both 40 mm long and coated with Pt to produce a focal length of 60 mm at 3 mrad incident angle, and collect up to a 120 µm by 120 µm incident X-ray beam with maximum angular acceptance of 2 mrad and a broad bandwidth of energies up to 30 keV. In an initial test a focal spot of about 150 nm in both horizontal and vertical directions was achieved with either polychromatic or monochromatic beam. The nested mirror geometry, with two mirrors mounted side-by-side and perpendicular to each other, is significantly more compact and provides higher demagnification than the traditional sequential KB mirror arrangement. Ultimately, nested mirrors can focus larger divergence to improve the diffraction limit of achromatic optics. A major challenge with the fabrication of the required mirrors is the need for near-perfect mirror surfaces near the edge of at least one of the mirrors. Special polishing procedures and surface profile coating were used to preserve the mirror surface quality at the reflecting edge. Further developments aimed at achieving diffraction-limited focusing below 50 nm are underway.

Measurement of persistence in YAG:Ce3+ scintillator with pulsed synchrotron X-rays

Matsuo, T. — 2011-07-01

The decay time of YAG:Ce3+ phosphor was studied using a CMOS camera with a frame rate of 1302000 s−1 and pulsed X-rays from SPring-8. A high-resolution X-ray detector with YAG:Ce3+ was used with the camera to view the focused beam from the helical undulator. Mismatch between the ring circulation time and the frame time gave rise to a periodic variation of beam intensity in successive frames. Analysis of data obtained with two bunch modes showed that the decay time of YAG:Ce3+ was 60 ns. The variation of the beam positions in isolated bunches was small enough to be neglected in experiments using the focused beam. The results also show the possibility of an X-ray diffraction study at high time and space resolution.

Hard X-ray Fourier transform holography from an array of oriented referenced objects

Iwamoto, H. — 2011-07-01

Hard X-ray Fourier transform holography (HXFTH) is a promising method for imaging nanoscale objects, including biological molecules, with a spatial resolution of a nanometer or better. However, it suffers from low scattering intensities being available for imaging owing to smaller object size and the low scattering cross section inherent in hard X-rays. One technique to overcome the problem would be to use an array of oriented objects, each with its own reference. Here the feasibility of this approach was experimentally tested by recording diffraction patterns from nanofabricated test patterns arranged in a 5 × 5 matrix. At an X-ray energy of 8 keV (λ = 1.55 Å), the image of the original test pattern was clearly restored with 60 s exposure on an imaging plate; the image was still recognizable with a 500 ms exposure on a CCD detector at the BL40XU beamline at SPring-8. The results demonstrate that the use of an array of referenced oriented objects for HXFTH is workable, and that it can be considered as a practical candidate for imaging biological molecules, identical particles of which are available but diffract even more weakly than artificially fabricated test patterns.

Radiation damage in room-temperature data acquisition with the PILATUS 6M pixel detector

Rajendran, C. — 2011-05-01

The first study of room-temperature macromolecular crystallography data acquisition with a silicon pixel detector is presented, where the data are collected in continuous sample rotation mode, with millisecond read-out time and no read-out noise. Several successive datasets were collected sequentially from single test crystals of thaumatin and insulin. The dose rate ranged between ∼1320 Gy s−1 and ∼8420 Gy s−1 with corresponding frame rates between 1.565 Hz and 12.5 Hz. The data were analysed for global radiation damage. A previously unreported negative dose-rate effect is observed in the indicators of global radiation damage, which showed an approximately 75% decrease in D1/2 at sixfold higher dose rate. The integrated intensity decreases in an exponential manner. Sample heating that could give rise to the enhanced radiation sensitivity at higher dose rate is investigated by collecting data between crystal temperatures of 298 K and 353 K. UV-Vis spectroscopy is used to demonstrate that disulfide radicals and trapped electrons do not accumulate at high dose rates in continuous data collection.

Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate

Karuppasamy, M. — 2011-05-01

Radiation damage is an important resolution limiting factor both in macromolecular X-ray crystallography and cryo-electron microscopy. Systematic studies in macromolecular X-ray crystallography greatly benefited from the use of dose, expressed as energy deposited per mass unit, which is derived from parameters including incident flux, beam energy, beam size, sample composition and sample size. In here, the use of dose is reintroduced for electron microscopy, accounting for the electron energy, incident flux and measured sample thickness and composition. Knowledge of the amount of energy deposited allowed us to compare doses with experimental limits in macromolecular X-ray crystallography, to obtain an upper estimate of radical concentrations that build up in the vitreous sample, and to translate heat-transfer simulations carried out for macromolecular X-ray crystallography to cryo-electron microscopy. Stroboscopic exposure series of 50–250 images were collected for different incident flux densities and integration times from Lumbricus terrestris extracellular hemoglobin. The images within each series were computationally aligned and analyzed with similarity metrics such as Fourier ring correlation, Fourier ring phase residual and figure of merit. Prior to gas bubble formation, the images become linearly brighter with dose, at a rate of approximately 0.1% per 10 MGy. The gradual decomposition of a vitrified hemoglobin sample could be visualized at a series of doses up to 5500 MGy, by which dose the sample was sublimed. Comparison of equal-dose series collected with different incident flux densities showed a dose-rate effect favoring lower flux densities. Heat simulations predict that sample heating will only become an issue for very large dose rates (50 e−Å−2 s−1 or higher) combined with poor thermal contact between the grid and cryo-holder. Secondary radiolytic effects are likely to play a role in dose-rate effects. Stroboscopic data collection combined with an improved understanding of the effects of dose and dose rate will aid single-particle cryo-electron microscopists to have better control of the outcome of their experiments.

Assessment of radiation damage behaviour in a large collection of empirically optimized datasets highlights the importance of unmeasured complicating effects

Krojer, T. — 2011-05-01

The radiation damage behaviour in 43 datasets of 34 different proteins collected over a year was examined, in order to gauge the reliability of decay metrics in practical situations, and to assess how these datasets, optimized only empirically for decay, would have benefited from the precise and automatic prediction of decay now possible with the programs RADDOSE [Murray, Garman & Ravelli (2004). J. Appl. Cryst. 37, 513–522] and BEST [Bourenkov & Popov (2010). Acta Cryst. D66, 409–419]. The results indicate that in routine practice the diffraction experiment is not yet characterized well enough to support such precise predictions, as these depend fundamentally on three interrelated variables which cannot yet be determined robustly and practically: the flux density distribution of the beam; the exact crystal volume; the sensitivity of the crystal to dose. The former two are not satisfactorily approximated from typical beamline information such as nominal beam size and transmission, or two-dimensional images of the beam and crystal; the discrepancies are particularly marked when using microfocus beams (<20 µm). Empirically monitoring decay with the dataset scaling B factor (Bourenkov & Popov, 2010) appears more robust but is complicated by anisotropic and/or low-resolution diffraction. These observations serve to delineate the challenges, scientific and logistic, that remain to be addressed if tools for managing radiation damage in practical data collection are to be conveniently robust enough to be useful in real time.

Correlated single-crystal electronic absorption spectroscopy and X-ray crystallography at NSLS beamline X26-C

Orville, A.M. — 2011-05-01

The research philosophy and new capabilities installed at NSLS beamline X26-C to support electronic absorption and Raman spectroscopies coupled with X-ray diffraction are reviewed. This beamline is dedicated full time to multidisciplinary studies with goals that include revealing the relationship between the electronic and atomic structures in macromolecules. The beamline instrumentation has been fully integrated such that optical absorption spectra and X-ray diffraction images are interlaced. Therefore, optical changes induced by X-ray exposure can be correlated with X-ray diffraction data collection. The installation of Raman spectroscopy into the beamline is also briefly reviewed. Data are now routinely generated almost simultaneously from three complementary types of experiments from the same sample. The beamline is available now to the NSLS general user population.

Current events

2011-03-01

Development of a hard X-ray delay line for X-ray photon correlation spectroscopy and jitter-free pump–probe experiments at X-ray free-electron laser sources

Roseker, W. — 2011-05-01

A hard X-ray delay line capable of splitting and delaying single X-ray pulses has been developed with the aim of performing X-ray photon correlation spectroscopy (XPCS) and X-ray pump–probe experiments at hard X-ray free-electron laser sources. The performance of the device was tested with 8.39 keV synchrotron radiation. Time delays up to 2.95 ns have been demonstrated. The feasibility of the device for performing XPCS studies was tested by recording static speckle patterns. The achieved speckle contrast of 56% indicates the possibility of performing ultra-fast XPCS studies with the delay line.

Revealing low-dose radiation damage using single-crystal spectroscopy

Owen, R.L. — 2011-05-01

The structural information and functional insight obtained from X-ray crystallography can be enhanced by the use of complementary spectroscopies. Here the information that can be obtained from spectroscopic methods commonly used in conjunction with X-ray crystallography and best-practice single-crystal UV-Vis absorption data collection are briefly reviewed. Using data collected with the in situ system at the Swiss Light Source, the time and dose scales of low-dose X-ray-induced radiation damage and solvated electron generation in metalloproteins at 100 K are investigated. The effect of dose rate on these scales is also discussed.

Additional phase information from UV damage of selenomethionine labelled proteins

Sanctis, D. de — 2011-05-01

Currently, selenium is the most widely used phasing vehicle for experimental phasing, either by single anomalous scattering or multiple-wavelength anomalous dispersion (MAD) procedures. The use of the single isomorphous replacement anomalous scattering (SIRAS) phasing procedure with selenomethionine containing proteins is not so commonly used, as it requires isomorphous native data. Here it is demonstrated that isomorphous differences can be measured from intensity changes measured from a selenium labelled protein crystal before and after UV exposure. These can be coupled with the anomalous signal from the dataset collected at the selenium absorption edge to obtain SIRAS phases in a UV-RIPAS phasing experiment. The phasing procedure for two selenomethionine proteins, the feruloyl esterase module of xylanase 10B from Clostridium thermocellum and the Mycobacterium tuberculosis chorismate synthase, have been investigated using datasets collected near the absorption edge of selenium before and after UV radiation. The utility of UV radiation in measuring radiation damage data for isomorphous differences is highlighted and it is shown that, after such measurements, the UV-RIPAS procedure yields comparable phase sets with those obtained from the conventional MAD procedure. The results presented are encouraging for the development of alternative phasing approaches for selenomethionine proteins in difficult cases.

Three-dimensional diffraction mapping by tuning the X-ray energy

Cornelius, T.W. — 2011-05-01

Three-dimensional reciprocal-space maps of a single SiGe island around the Si(004) Bragg peak are recorded using an energy-tuning technique with a microfocused X-ray beam with compound refractive lenses as focusing optics. The map is in agreement with simulated data as well as with a map recorded by an ordinary rocking-curve scan. The energy-tuning approach circumvents both the comparatively large sphere of confusion of diffractometers compared with nanostructures and vibrations induced by motors. Thus, this method offers new possibilities for novel combinations of three-dimensional micro- and nano-focused X-ray diffraction with complex in situ sample environments such as scanning probe microscopes.

Fast X-ray microdiffraction techniques for studying irreversible transformations in materials

Kelly, S.T. — 2011-05-01

A pair of techniques have been developed for performing time-resolved X-ray microdiffraction on irreversible phase transformations. In one technique capillary optics are used to focus a high-flux broad-spectrum X-ray beam to a 60 µm spot size and a fast pixel array detector is used to achieve temporal resolution of 55 µs. In the second technique the X-rays are focused with Kirkpatrick–Baez mirrors to achieve a spatial resolution better than 10 µm and a fast shutter is used to provide temporal resolution better than 20 µs while recording the diffraction pattern on a (relatively slow) X-ray CCD camera. Example data from experiments are presented where these techniques are used to study self-propagating high-temperature synthesis reactions in metal laminate foils.

High-efficiency Fresnel zone plates for hard X-rays by 100 keV e-beam lithography and electroplating

Gorelick, S. — 2011-05-01

The fabrication and characterization of Fresnel zone plates (FZPs) for hard X-ray microscopy applications are reported. High-quality 500 nm- and 1 µm-thick Au FZPs with outermost zone widths down to 50 nm and 70 nm, respectively, and with diameters up to 600 µm were fabricated. The diffraction efficiencies of the fabricated FZPs were measured for a wide range of X-ray energies (2.8–13.2 keV) showing excellent values up to 65–75% of the theoretical values, reflecting the good quality of the FZPs. Spatially resolved diffraction efficiency measurements indicate the uniformity of the FZPs and a defect-free structure.

Experimental procedure for the characterization of radiation damage in macromolecular crystals

Leal, R.M.F. — 2011-05-01

A reliable and reproducible method to automatically characterize the radiation sensitivity of macromolecular crystals at the ESRF beamlines has been developed. This new approach uses the slope of the linear dependence of the overall isotropic B-factor with absorbed dose as the damage metric. The method has been implemented through an automated procedure using the EDNA on-line data analysis framework and the MxCuBE data collection control interface. The outcome of the procedure can be directly used to design an optimal data collection strategy. The results of tests carried out on a number of model and real-life crystal systems are presented.

New developments in fabrication of high-energy-resolution analyzers for inelastic X-ray spectroscopy

Said, A.H. — 2011-05-01

In this work new improvements related to the fabrication of spherical bent analyzers for 1 meV energy-resolution inelastic X-ray scattering spectroscopy are presented. The new method includes the use of a two-dimensional bender to achieve the required radius of curvature for X-ray analyzers. The advantage of this method is the ability to monitor the focus during bending, which leads to higher-efficiency analyzers.

Multi-frame acquisition scheme for efficient energy-dispersive X-ray magnetic circular dichroism in pulsed high magnetic fields at the Fe K-edge

Strohm, C. — 2011-03-01

Using a fast silicon strip detector, a multi-frame acquisition scheme was implemented to perform energy-dispersive X-ray magnetic circular dichroism at the iron K-edge in pulsed high magnetic fields. The acquisition scheme makes use of the entire field pulse. The quality of the signal obtained from samples of ferrimagnetic erbium iron garnet allows for quantitative evaluation of the signal amplitude. Below the compensation point, two successive field-induced phase transitions and the reversal of the net magnetization of the iron sublattices in the intermediate phase were observed.

Numerical optimization of spherical variable-line-spacing grating X-ray spectrometers

Strocov, V.N. — 2011-03-01

Operation of an X-ray spectrometer based on a spherical variable-line-spacing (VLS) grating is analyzed using dedicated ray-tracing software allowing fast optimization of the grating parameters and spectrometer geometry. The analysis is illustrated with optical design of a model spectrometer to deliver a resolving power above 20400 at a photon energy of 930 eV (Cu L-edge). With this energy taken as reference, the VLS coefficients are optimized to cancel the lineshape asymmetry (mostly from the coma aberrations) as well as minimize the symmetric aberration broadening at large grating illuminations, dramatically increasing the aberration-limited vertical acceptance of the spectrometer. For any energy away from the reference, corrections to the entrance arm and light incidence angle on the grating are evaluated to maintain the exactly symmetric lineshape. Furthermore, operational modes when these corrections are coordinated are evaluated to maintain either energy-independent focal curve inclination or maximal aberration-limited spectrometer acceptance. The results are supported by analytical evaluation of the coma term of the optical path function. This analysis thus gives a recipe for designing a high-resolution spherical VLS grating spectrometer operating with negligible aberrations at large acceptance and over an extended energy range.

Assessment of chemical species of lead accumulated in tidemarks of human articular cartilage by X-ray absorption near-edge structure analysis

Meirer, F. — 2011-03-01

A highly specific accumulation of the toxic element lead was recently measured in the transition zone between non-calcified and calcified normal human articular cartilage. This transition zone, the so-called `tidemark', is considered to be an active calcification front of great clinical importance. However, little is known about the mechanisms of accumulation and the chemical form of Pb in calcified cartilage and bone. Using spatially resolved X-ray absorption near-edge structure analysis (µ-XANES) at the Pb L3-edge, the chemical state of Pb in the osteochondral region was investigated. The feasibility of the µ-XANES set-up at the SUL-X beamline (ANKA synchrotron light source) was tested and confirmed by comparing XANES spectra of bulk Pb-reference compounds recorded at both the XAS and the SUL-X beamline at ANKA. The µ-XANES set-up was then used to investigate the tidemark region of human bone (two patella samples and one femoral head sample). The spectra recorded at the tidemark and at the trabecular bone were found to be highly correlated with the spectra of synthetic Pb-doped carbonated hydroxyapatite, suggesting that in both of these very different tissues Pb is incorporated into the hydroxyapatite structure.

Coherent diffraction microscopy at SPring-8: instrumentation, data acquisition and data analysis

Xu, R. — 2011-03-01

Since the first demonstration of coherent diffraction microscopy in 1999, this lensless imaging technique has been experimentally refined by continued developments. Here, instrumentation and experimental procedures for measuring oversampled diffraction patterns from non-crystalline specimens using an undulator beamline (BL29XUL) at SPring-8 are presented. In addition, detailed post-experimental data analysis is provided that yields high-quality image reconstructions. As the acquisition of high-quality diffraction patterns is at least as important as the phase-retrieval procedure to guarantee successful image reconstructions, this work will be of interest for those who want to apply this imaging technique to materials science and biological samples.

Current events

2011-01-01

A simplified description of X-ray free-electron lasers

Margaritondo, G. — 2011-03-01

It is shown that an elementary semi-quantitative approach explains essential features of the X-ray free-electron laser mechanism, in particular those of the gain and saturation lengths. Using mathematical methods and derivations simpler than complete theories, this treatment reveals the basic physics that dominates the mechanism and makes it difficult to realise free-electron lasers for short wavelengths. This approach can be specifically useful for teachers at different levels and for colleagues interested in presenting X-ray free-electron lasers to non-specialized audiences.

MicroGISAXS of Langmuir–Blodgett protein films: effect of temperature on long-range order. Addendum

Pechkova, E. — 2011-03-01

An extra acknowledgment is published for the paper by Pechkova et al. [(2009), J. Synchrotron Rad. 16, 330–335].

High-throughput full-automatic synchrotron-based tomographic microscopy

Mader, K. — 2011-03-01

At the TOMCAT (TOmographic Microscopy and Coherent rAdiology experimenTs) beamline of the Swiss Light Source with an energy range of 8–45 keV and voxel size from 0.37 µm to 7.4 µm, full tomographic datasets are typically acquired in 5 to 10 min. To exploit the speed of the system and enable high-throughput studies to be performed in a fully automatic manner, a package of automation tools has been developed. The samples are automatically exchanged, aligned, moved to the correct region of interest, and scanned. This task is accomplished through the coordination of Python scripts, a robot-based sample-exchange system, sample positioning motors and a CCD camera. The tools are suited for any samples that can be mounted on a standard SEM stub, and require no specific environmental conditions. Up to 60 samples can be analyzed at a time without user intervention. The throughput of the system is dependent on resolution, energy and sample size, but rates of four samples per hour have been achieved with 0.74 µm voxel size at 17.5 keV. The maximum intervention-free scanning time is theoretically unlimited, and in practice experiments have been running unattended as long as 53 h (the average beam time allocation at TOMCAT is 48 h per user). The system is the first fully automated high-throughput tomography station: mounting samples, finding regions of interest, scanning and reconstructing can be performed without user intervention. The system also includes many features which accelerate and simplify the process of tomographic microscopy.

Quick-EXAFS implementation on the general purpose EXAFS beamline at ESRF

Prestipino, C. — 2011-03-01

The new implementation of QEXAFS acquisition on the general purpose EXAFS beamline BM29 at the European Synchrotron Radiation Facility is presented. By adopting a continuous-scan mode, a high signal-to-noise ratio can be maintained, together with a fixed exit beam and full compatibility with step-by-step operation, while reducing acquisition times to a few seconds. The new equipment implemented on the beamline is described and the potential of this application is demonstrated with a few examples.

Phosphorus K-edge XANES spectroscopy of mineral standards

Ingall, E.D. — 2011-03-01

Phosphorus K-edge X-ray absorption near-edge structure (XANES) spectroscopy was performed on phosphate mineral specimens including (a) twelve specimens from the apatite group covering a range of compositional variation and crystallinity; (b) six non-apatite calcium-rich phosphate minerals; (c) 15 aluminium-rich phosphate minerals; (d) ten phosphate minerals rich in either reduced iron or manganese; (e) four phosphate minerals rich in either oxidized iron or manganese; (f) eight phosphate minerals rich in either magnesium, copper, lead, zinc or rare-earth elements; and (g) four uranium phosphate minerals. The identity of all minerals examined in this study was independently confirmed using X-ray powder diffraction. Minerals were distinguished using XANES spectra with a combination of pre-edge features, edge position, peak shapes and post-edge features. Shared spectral features were observed in minerals with compositions dominated by the same specific cation. Analyses of apatite-group minerals indicate that XANES spectral patterns are not strongly affected by variations in composition and crystallinity typical of natural mineral specimens.

Comparison of lens- and fiber-coupled CCD detectors for X-ray computed tomography

Uesugi, K. — 2011-03-01

X-ray imaging detectors with an identical phosphor and a CCD chip but employing lens- and fiber-coupling between them have been compared. These are designed for X-ray imaging experiments, especially computed tomography, at the medium-length beamline at the SPring-8 synchrotron radiation facility. It was found that the transmittance of light to the CCD is about four times higher in the fiber-coupled detector. The uniformity of response in the lens-coupled detector has a global shading of up to 40%, while pixel-to-pixel variation owing to a chicken-wire pattern was dominant in the fiber-coupled detector. Apart from the higher transmittance, the fiber-coupled detector has a few characteristics that require attention when it is used for computed tomography, which are browning of the fiber, discontinuity in the image, image distortion, and dark spots in the chicken-wire pattern. Thus, it is most suitable for high-speed tomography of samples that tend to deform, for example biological and soft materials.

X-ray transfocators: focusing devices based on compound refractive lenses

Vaughan, G.B.M. — 2011-03-01

This paper describes a tunable X-ray focusing apparatus, referred to as a transfocator, based on compound refractive lenses. By varying the number of lenses in the beam, the X-ray energy focused and the focal length can be varied continuously throughout a large range of energies and distances. The instrument can be used in both white and monochromatic beams to focus, pre-focus or collimate the beam. The transfocator can be used with other monochromators and/or other focusing elements, leading to significant increases in flux. Furthermore, the chromatic nature of the focusing means the transfocator suppresses harmonics and can also be used as an extremely high flux broad-band-pass monochromator. These devices have been installed in the first optics and second experimental hutches at the ID11 beamline at the ESRF.

Diffraction structural biology – introductory overview

Fourme, R. — 2011-01-01

An introductory overview to the special issue papers on diffraction structural biology in this issue of the journal.

A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

Fourme, R. — 2011-01-01

Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

Three-dimensional X-ray micro-velocimetry

Lee, W.-K. — 2011-03-01

A direct measurement of three-dimensional X-ray velocimetry with micrometer spatial resolution is presented. The key to this development is the use of a Laue crystal as an X-ray beam splitter and mirror. Three-dimensional flow velocities in a 0.4 mm-diameter tubing were recorded, with <5 µm spatial resolution and speeds of 0.7 mm s−1. This development paves the way for three-dimensional velocimetry in many cases where visible-light techniques are not effective, such as multiphase flow or flow of optically opaque liquids.

Current events

2010-11-01

Synchrotron Mössbauer spectroscopy using high-speed shutters

Toellner, T.S. — 2011-03-01

A new method of performing Mössbauer spectroscopy with synchrotron radiation is demonstrated that involves using a high-speed periodic shutter near the focal spot of a microfocused X-ray beam. This fast microshuttering technique operates without a high-resolution monochromator and has the potential to produce much higher signal rates. It also offers orders of magnitude more suppression of unwanted electronic charge scattering. Measurement results are shown that prove the principle of the method and improvements are discussed to deliver a very pure beam of Mössbauer photons (E/ΔE ≃ 1012) with previously unavailable spectral brightness. Such a source will allow both Mössbauer spectroscopy in the energy domain with the many advantageous characteristics of synchrotron radiation and new opportunities for measurements using X-rays with ultra-high energy resolution.

Indirectly illuminated X-ray area detector for X-ray photon correlation spectroscopy

Shinohara, Y. — 2010-11-01

An indirectly illuminated X-ray area detector is employed for X-ray photon correlation spectroscopy (XPCS). The detector consists of a phosphor screen, an image intensifier (microchannel plate), a coupling lens and either a CCD or CMOS image sensor. By changing the gain of the image intensifier, both photon-counting and integrating measurements can be performed. Speckle patterns with a high signal-to-noise ratio can be observed in a single shot in the integrating mode, while XPCS measurement can be performed with much fewer photons in the photon-counting mode. By switching the image sensor, various combinations of frame rate, dynamic range and active area can be obtained. By virtue of these characteristics, this detector can be used for XPCS measurements of various types of samples that show slow or fast dynamics, a high or low scattering intensity, and a wide or narrow range of scattering angles.

Improvement in the quality of hematopoietic prostaglandin D synthase crystals in a microgravity environment

Tanaka, H. — 2011-01-01

Human hematopoietic prostaglandin synthase, one of the better therapeutic target enzymes for allergy and inflammation, was crystallized with 22 inhibitors and in three inhibitor-free conditions in microgravity. Most of the space-grown crystals showed better X-ray diffraction patterns than the terrestrially grown ones, indicating the advantage of a microgravity environment on protein crystallization, especially in the case of this protein.

Using lanthanoid complexes to phase large macromolecular assemblies

Talon, R. — 2011-01-01

Lanthanoid ions exhibit extremely large anomalous X-ray scattering at their LIII absorption edge. They are thus well suited for anomalous diffraction experiments. A novel class of lanthanoid complexes has been developed that combines the physical properties of lanthanoid atoms with functional chemical groups that allow non-covalent binding to proteins. Two structures of large multimeric proteins have already been determined by using such complexes. Here the use of the luminescent europium tris-dipicolinate complex [Eu(DPA)3]3− to solve the low-resolution structure of a 444 kDa homododecameric aminopeptidase, called PhTET1-12s from the archaea Pyrococcus horikoshii, is reported. Surprisingly, considering the low resolution of the data, the experimental electron density map is very well defined. Experimental phases obtained by using the lanthanoid complex lead to maps displaying particular structural features usually observed in higher-resolution maps. Such complexes open a new way for solving the structure of large molecular assemblies, even with low-resolution data.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

Bui, K.H. — 2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed.

Biomolecular solution X-ray scattering at the National Synchrotron Light Source

Allaire, M. — 2011-01-01

In recent years there has been a growing interest in the application of X-ray scattering techniques to biomolecules in solution. At NSLS, a new undulator-based beamline, X9, has been constructed to address the oversubscribed user demand for X-ray scattering. Beamline X9 has the capability to perform small/wide-angle X-ray scattering (SAXS/WAXS) all in one single instrument. This is accomplished by utilizing a vacuum sample/detector chamber that is an integral part of the SAXS scattering flight path. This vacuum chamber allows a WAXS detector to be positioned at a close distance from the sample, while not interfering with scattered X-rays at small angles from reaching the SAXS detector. A regular training program, the X9 workbench, has also been established to allow users to become familiar with beamline X9 for solution X-ray scattering.

Structural insights and ab initio sequencing within the DING proteins family

Elias, M. — 2011-01-01

DING proteins constitute an intriguing family of phosphate-binding proteins that was identified in a wide range of organisms, from prokaryotes and archae to eukaryotes. Despite their seemingly ubiquitous occurrence in eukaryotes, their encoding genes are missing from sequenced genomes. Such a lack has considerably hampered functional studies. In humans, these proteins have been related to several diseases, like atherosclerosis, kidney stones, inflammation processes and HIV inhibition. The human phosphate binding protein is a human representative of the DING family that was serendipitously discovered from human plasma. An original approach was developed to determine ab initio the complete and exact sequence of this 38 kDa protein by utilizing mass spectrometry and X-ray data in tandem. Taking advantage of this first complete eukaryotic DING sequence, a immunohistochemistry study was undertaken to check the presence of DING proteins in various mice tissues, revealing that these proteins are widely expressed. Finally, the structure of a bacterial representative from Pseudomonas fluorescens was solved at sub-angstrom resolution, allowing the molecular mechanism of the phosphate binding in these high-affinity proteins to be elucidated.

Optimization of salt concentration in PEG-based crystallization solutions

Yamanaka, M. — 2011-01-01

Although polyethylene glycol (PEG) is the most widely used precipitant in protein crystallization, the concentration of co-existing salt in the solution has not been well discussed. To determine the optimum salt concentration range, several kinds of protein were crystallized in a 30% PEG 4000 solution at various NaCl concentrations with various pH levels. It was found that, if crystallization occurred, the lowest effective salt concentration depended on the pH of the protein solution and the pI of the protein molecule; that is, higher salt concentrations were required for crystal growth if the difference between pH and pI was increasing. The linear relationship between the charge density of the protein and the ionic strength of the crystallization solution was further verified. These results suggested that the lowest effective concentration of salt in a crystallization solution can be predicted before performing a crystallization experiment. Our results can be a tip for tuning crystallization conditions by the vapor-diffusion method.

Microcrystallography, high-pressure cryocooling and BioSAXS at MacCHESS

Englich, U. — 2011-01-01

The Macromolecular Diffraction Facility at the Cornell High Energy Synchrotron Source (MacCHESS) is a national research resource supported by the National Center for Research Resources of the US National Institutes of Health. MacCHESS is pursuing several research initiatives designed to benefit both CHESS users and the wider structural biology community. Three initiatives are presented in further detail: microcrystallography, which aims to improve the collection of diffraction data from crystals a few micrometers across, or small well diffracting regions of inhomogeneous crystals, so as to obtain high-resolution structures; pressure cryocooling, which can stabilize transient structures and reduce lattice damage during the cooling process; and BioSAXS (small-angle X-ray scattering on biological solutions), which can extract molecular shape and other structural information from macromolecules in solution.

Detection of the reaction intermediates catalyzed by a copper amine oxidase

Kataoka, M. — 2011-01-01

To reveal the chemical changes and geometry changes of active-site residues that cooperate with a reaction is important for understanding the functional mechanism of proteins. Consecutive temporal analyses of enzyme structures have been performed during reactions to clarify structure-based reaction mechanisms. Phenylethylamine oxidase from Arthrobacter globiformis (AGAO) contains a copper ion and topaquinone (TPQox). The catalytic reaction of AGAO catalyzes oxidative deaminations of phenylethylamine and consists of reductive and oxidative half-reactions. In the reduction step, TPQox reacts with a phenylethylamine (PEA) substrate giving rise to a topasemiquinone (TPQsq) formed Schiff-base and produces phenylacetaldehyde. To elucidate the mechanism of the reductive half-reaction, an attempt was made to trap the reaction intermediates in order to analyze their structures. The reaction proceeded within the crystals when AGAO crystals were soaked in a PEA solution and freeze-trapped in liquid nitrogen. The reaction stage of each crystal was confirmed by single-crystal microspectrometry, before X-ray diffraction measurements were made of four reaction intermediates. The structure at 15 min after the onset of the reaction was analyzed at atomic resolution, and it was shown that TPQox and some residues in the substrate channel were alternated via catalytic reductive half-reactions.

Deriving the ultrastructure of α-crustacyanin using lower-resolution structural and biophysical methods

Rhys, N.H. — 2011-01-01

The low-resolution structure of α-crustacyanin has been determined to 30 Å resolution using negative-stain electron microscopy (EM) with single-particle averaging. The protein, which is an assembly of eight β-crustacyanin dimers, appears asymmetrical and rather open in layout. A model was built to the EM map using the X-ray crystallographic structure of β-crustacyanin guided by PISA interface analyses. The model has a theoretical sedimentation coefficient that matches well with the experimentally derived value from sedimentation velocity analytical ultracentrifugation. Additionally, the EM model has similarities to models calculated independently by rigid-body modelling to small-angle X-ray scattering (SAXS) data and extracted in silico from the β-crustacyanin crystal lattice. Theoretical X-ray scattering from each of these models is in reasonable agreement with the experimental SAXS data and together suggest an overall design for the α-crustacyanin assembly.

Approach for growth of high-quality and large protein crystals

Matsumura, H. — 2011-01-01

Three crystallization methods for growing large high-quality protein crystals, i.e. crystallization in the presence of a semi-solid agarose gel, top-seeded solution growth (TSSG) and a large-scale hanging-drop method, have previously been presented. In this study the effectiveness of crystallization in the presence of a semi-solid agarose gel has been further evaluated by crystallizing additional proteins in the presence of 2.0% (w/v) agarose gel, resulting in complete gelification with high mechanical strength. In TSSG the seed crystals are hung by a seed holder protruding from the top of the growth vessel to prevent polycrystallization. In the large-scale hanging-drop method, a cut pipette tip was used to maintain large-scale droplets consisting of protein–precipitant solution. Here a novel crystallization method that combines TSSG and the large-scale hanging-drop method is reported. A large and single crystal of lysozyme was obtained by this method.

Structure of the inhibitor complex of old yellow enzyme from Trypanosoma cruzi

Yamaguchi, K. — 2011-01-01

Old yellow enzyme (OYE) is an NADPH oxidoreductase which contains flavin mononucleotide as prosthetic group. The X-ray structures of OYE from Trypanosoma cruzi (TcOYE) which produces prostaglandin (PG) F2α from PGH2 have been determined in the presence or absence of menadione. The binding motif of menadione, known as one of the inhibitors for TcOYE, should accelerate the structure-based development of novel anti-chagasic drugs that inhibit PGF2α production specifically.

Single-crystal Raman spectroscopy and X-ray crystallography at beamline X26-C of the NSLS

Stoner-Ma, D. — 2011-01-01

Three-dimensional structures derived from X-ray diffraction of protein crystals provide a wealth of information. Features and interactions important for the function of macromolecules can be deduced and catalytic mechanisms postulated. Still, many questions can remain, for example regarding metal oxidation states and the interpretation of `mystery density', i.e. ambiguous or unknown features within the electron density maps, especially at ∼2 Å resolutions typical of most macromolecular structures. Beamline X26-C at the National Synchrotron Light Source (NSLS), Brookhaven National Laboratory (BNL), provides researchers with the opportunity to not only determine the atomic structure of their samples but also to explore the electronic and vibrational characteristics of the sample before, during and after X-ray diffraction data collection. When samples are maintained under cryo-conditions, an opportunity to promote and follow photochemical reactions in situ as a function of X-ray exposure is also provided. Plans are in place to further expand the capabilities at beamline X26-C and to develop beamlines at NSLS-II, currently under construction at BNL, which will provide users access to a wide array of complementary spectroscopic methods in addition to high-quality X-ray diffraction data.

Current events

2010-09-01

Protein surface shielding agents in protein crystallization

Hašek, J. — 2011-01-01

The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds.

Software for the high-throughput collection of SAXS data using an enhanced Blu-Ice/DCS control system

Classen, S. — 2010-11-01

Biological small-angle X-ray scattering (SAXS) provides powerful complementary data for macromolecular crystallography (MX) by defining shape, conformation and assembly in solution. Although SAXS is in principle the highest throughput technique for structural biology, data collection is limited in practice by current data collection software. Here the adaption of beamline control software, historically developed for MX beamlines, for the efficient operation and high-throughput data collection at synchrotron SAXS beamlines is reported. The Blu-Ice GUI and Distributed Control System (DCS) developed in the Macromolecular Crystallography Group at the Stanford Synchrotron Radiation Laboratory has been optimized, extended and enhanced to suit the specific needs of the biological SAXS endstation at the SIBYLS beamline at the Advanced Light Source. The customizations reported here provide a potential route for other SAXS beamlines in need of robust and efficient beamline control software. As a great deal of effort and optimization has gone into crystallographic software, the adaption and extension of crystallographic software may prove to be a general strategy to provide advanced SAXS software for the synchrotron community. In this way effort can be put into optimizing features for SAXS rather than reproducing those that have already been successfully implemented for the crystallographic community.

Structure analysis of group I plant nucleases

Dohnálek, J. — 2011-01-01

Anticancer drugs attacking nucleic acids of the target cells have so far been based on animal or fungal ribonucleases. Plant nucleases have been proved to exhibit decreased cytotoxic side effects. Tomato bifunctional nuclease 1 with activity against both single-stranded and double-stranded RNA and DNA was produced in tobacco leaves as recombinant protein. The enzyme crystallizes under several different crystallization conditions. The presence of Zn2+ ions was confirmed by X-ray fluorescence. First crystallographic data were obtained.

The alternating access mechanism of transport as observed in the sodium-hydantoin transporter Mhp1

Weyand, S. — 2011-01-01

Secondary active transporters move molecules across cell membranes by coupling this process to the energetically favourable downhill movement of ions or protons along an electrochemical gradient. They function by the alternating access model of transport in which, through conformational changes, the substrate binding site alternately faces either side of the membrane. Owing to the difficulties in obtaining the crystal structure of a single transporter in different conformational states, relatively little structural information is known to explain how this process occurs. Here, the structure of the sodium-benzylhydantoin transporter, Mhp1, from Microbacterium liquefaciens, has been determined in three conformational states; from this a mechanism is proposed for switching from the outward-facing open conformation through an occluded structure to the inward-facing open state.

Research and development of an electron beam focusing system for a high-brightness X-ray generator

Sakai, T. — 2011-01-01

A new type of rotating anticathode X-ray generator, where an electron beam of up to 60 keV irradiates the inner surface of a U-shaped Cu anticathode, has achieved a beam brilliance of 130 kW mm−2 (at 2.3 kW). A higher-flux electron beam is expected from simulation by optimizing the geometry of a combined-function-type magnet instead of the fringing field of the bending magnet. In order to minimize the size of the X-ray source the electron beam has been focused over a short distance by a new combined-function bending magnet, whose geometrical shape was determined by simulation using the Opera-3D, General Particle Tracer and CST-STUDIO codes. The result of the simulation clearly shows that the role of combined functions in both the bending and the steering magnets is important for focusing the beam to a small size. FWHM sizes of the beam are predicted by simulation to be 0.45 mm (horizontal) and 0.05 mm (vertical) for a 120 keV/75 mA beam, of which the effective brilliance is about 500 kW mm−2 on the supposition of a two-dimensional Gaussian distribution. High-power tests have begun using a high-voltage 120 kV/75 mA power supply for the X-ray generator instead of 60 kV/100 mA. The beam focus size on the target will be verified in the experiments.

Crystal structure of stable protein CutA1 from psychrotrophic bacterium Shewanella sp. SIB1

Sato, A. — 2011-01-01

CutA1 is widely found in bacteria, plants and animals, including humans. The functions of CutA1, however, have not been well clarified. It is known that CutA1s from Pyrococcus horikoshii, Thermus thermophilus and Oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. In this work the crystal structure of CutA1 from the psychrotrophic bacterium Shewanella sp. SIB1 (SIB1–CutA1) in a trimeric form was determined at 2.7 Å resolution. This is the first crystal structure of a psychrotrophic CutA1. The overall structure of SIB1–CutA1 is similar to those of CutA1 from Homo sapiens, Escherichia coli, Pyrococcus horikoshii, Thermus thermophilus, Termotoga maritima, Oryza sativa and Rattus norvergicus. A peculiarity is observed in the β2 strand. The β2 strand is divided into two short β strands, β2a and β2b, in SIB1–CutA1. A thermal denaturation experiment revealed that SIB1–CutA1 does not unfold completely at 363 K at pH 7.0, although Shewanella sp. SIB1 cannot grow at temperatures exceeding 303 K. These results indicate that the trimeric structural motif of CutA1 is the critical factor in its unusually high stability and suggest that CutA1 needs to maintain its high stability in order to function, even in psychrotrophs.

UV LED lighting for automated crystal centring

Chavas, L.M.G. — 2011-01-01

A direct outcome of the exponential growth of macromolecular crystallography is the continuously increasing demand for synchrotron beam time, both from academic and industrial users. As more and more projects entail screening a profusion of sample crystals, fully automated procedures at every level of the experiments are being implemented at all synchrotron facilities. One of the major obstacles to achieving such automation lies in the sample recognition and centring in the X-ray beam. The capacity of UV light to specifically react with aromatic residues present in proteins or with DNA base pairs is at the basis of UV-assisted crystal centring. Although very efficient, a well known side effect of illuminating biological samples with strong UV sources is the damage induced on the irradiated samples. In the present study the effectiveness of a softer UV light for crystal centring by taking advantage of low-power light-emitting diode (LED) sources has been investigated. The use of UV LEDs represents a low-cost solution for crystal centring with high specificity.

Beam-induced damage on diffractive hard X-ray optics

Nygård, K. — 2010-11-01

The issue of beam-induced damage on diffractive hard X-ray optics is addressed. For this purpose a systematic study on the radiation damage induced by a high-power X-ray beam is carried out in both ambient and inert atmospheres. Diffraction gratings fabricated by three different techniques are considered: electroplated Au gratings both with and without the polymer mold, and Ir-coated Si gratings. The beam-induced damage is monitored by X-ray diffraction and evaluated using scanning electron microscopy.

A new technique to examine individual pollutant particle and fibre deposition and transit behaviour in live mouse trachea

Donnelley, M. — 2010-11-01

During respiration, particles suspended in the air are inhaled and unless cleared by airway defences they can remain and affect lung health. Their size precludes the use of standard imaging modalities so we have developed synchrotron phase-contrast X-ray imaging (PCXI) methods to non-invasively monitor the behaviour of individual particles in live mouse airways. In this study we used these techniques to examine post-deposition particle behaviour in the trachea. PCXI was used to monitor the deposition and subsequent behaviour of particles of quarry dust and lead ore; fibres of asbestos and fibreglass; and hollow glass micro-spheres. Visibility was examined in vitro and ex vivo to avoid the complicating effects of surrounding tissue and respiratory or cardiac motion. Particle behaviour was then examined after deposition onto the tracheal airway surfaces of live mice. Each particle and fibre looked and behaved differently on the airway surface. Particles lodged on the airway shortly after deposition, and the rate at which this occurred was dependent on the particle type and size. After the live-imaging experiments, excised airway samples were examined using light and electron microscopy. Evidence of particle capture into the airway surface fluids and the epithelial cell layer was found. PCXI is a valuable tool for examining post-deposition particulate behaviour in the tracheal airway. These first indications that the interaction between airways and individual particles may depend on the particle type and size should provide a novel approach to studying the early effects of respired particles on airway health.

Raster microdiffraction with synchrotron radiation of hydrated biopolymers with nanometre step-resolution: case study of starch granules

Riekel, C. — 2010-11-01

X-ray radiation damage propagation is explored for hydrated starch granules in order to reduce the step resolution in raster-microdiffraction experiments to the nanometre range. Radiation damage was induced by synchrotron radiation microbeams of 5, 1 and 0.3 µm size with ∼0.1 nm wavelength in B-type potato, Canna edulis and Phajus grandifolius starch granules. A total loss of crystallinity of granules immersed in water was found at a dose of ∼1.3 photons nm−3. The temperature dependence of radiation damage suggests that primary radiation damage prevails up to about 120 K while secondary radiation damage becomes effective at higher temperatures. Primary radiation damage remains confined to the beam track at 100 K. Propagation of radiation damage beyond the beam track at room temperature is assumed to be due to reactive species generated principally by water radiolysis induced by photoelectrons. By careful dose selection during data collection, raster scans with 500 nm step-resolution could be performed for granules immersed in water.

Crystallization and preliminary structural analysis of the giant haemoglobin from Glossoscolex paulistus at 3.2 Å

Bachega, J.F.R. — 2011-01-01

Glossoscolex paulistus is a free-living earthworm encountered in south-east Brazil. Its oxygen transport requirements are undertaken by a giant extracellular haemoglobin, or erythrocruorin (HbGp), which has an approximate molecular mass of 3.6 MDa and, by analogy with its homologue from Lumbricus terrestris (HbLt), is believed to be composed of a total of 180 polypeptide chains. In the present work the full 3.6 MDa particle in its cyanomet state was purified and crystallized using sodium citrate or PEG8000 as precipitant. The crystals contain one-quarter of the full particle in the asymmetric unit of the I222 cell and have parameters of a = 270.8 Å, b = 320.3 Å and c = 332.4 Å. Diffraction data were collected to 3.15 Å using synchrotron radiation on beamline X29A at the Brookhaven National Laboratory and represent the highest resolution data described to date for similar erythrocruorins. The structure was solved by molecular replacement using a search model corresponding to one-twelfth of its homologue from HbLt. This revealed that HbGp belongs to the type I class of erythrocruorins and provided an interpretable initial electron density map in which many features including the haem groups and disulfide bonds could be identified.

Purine nucleoside phosphorylase from Schistosoma mansoni in complex with ribose-1-phosphate

D'Muniz Pereira, H. — 2011-01-01

Schistosomes are blood flukes which cause schistosomiasis, a disease affecting approximately 200 million people worldwide. Along with several other important human parasites including trypanosomes and Plasmodium, schistosomes lack the de novo pathway for purine synthesis and depend exclusively on the salvage pathway for their purine requirements, making the latter an attractive target for drug development. Part of the pathway involves the conversion of inosine (or guanosine) into hypoxanthine (or guanine) together with ribose-1-phosphate (R1P) or vice versa. This inter-conversion is undertaken by the enzyme purine nucleoside phosphorylase (PNP) which has been used as the basis for the development of novel anti-malarials, conceptually validating this approach. It has been suggested that, during the reverse reaction, R1P binding to the enzyme would occur only as a consequence of conformational changes induced by hypoxanthine, thus making a binary PNP–R1P complex unlikely. Contradictory to this statement, a crystal structure of just such a binary complex involving the Schistosoma mansoni enzyme has been successfully obtained. The ligand shows an intricate hydrogen-bonding network in the phosphate and ribose binding sites and adds a further chapter to our knowledge which could be of value in the future development of selective inhibitors.

The MYTHEN detector for X-ray powder diffraction experiments at the Swiss Light Source

Bergamaschi, A. — 2010-09-01

The MYTHEN single-photon-counting silicon microstrip detector has been developed at the Swiss Light Source for time-resolved powder diffraction experiments. An upgraded version of the detector has been installed at the SLS powder diffraction station allowing the acquisition of diffraction patterns over 120° in 2θ in fractions of seconds. Thanks to the outstanding performance of the detector and to the calibration procedures developed, the quality of the data obtained is now comparable with that of traditional high-resolution point detectors in terms of FWHM resolution and peak profile shape, with the additional advantage of fast and simultaneous acquisition of the full diffraction pattern. MYTHEN is therefore optimal for time-resolved or dose-critical measurements. The characteristics of the MYTHEN detector together with the calibration procedures implemented for the optimization of the data are described in detail. The refinements of two known standard powders are discussed together with a remarkable application of MYTHEN to organic compounds in relation to the problem of radiation damage.

The role of single element errors in planar parabolic compound refractive lenses

Andrejczuk, A. — 2010-09-01

The propagation of X-rays through a compound refractive lens (CRL) with imperfect CRL elements is investigated. The trajectories of random rays within the geometrical optics regime are calculated in one plane using Monte Carlo methods. Three different lenses were simulated: Be, Al and Ni lenses designed for photon energies of 20 keV, 60 keV and 175 keV, respectively. The results show that while transverse displacements of single elements in a CRL do not influence imaging resolution, rotational errors can be important. Systematic calculations of aberrations owing to the deviation of the element's surface from a perfect parabolic shape are also presented.

Current events

2010-07-01

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

Gabadinho, J. — 2010-09-01

The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1.

High-resolution soft X-ray beamline ADRESS at the Swiss Light Source for resonant inelastic X-ray scattering and angle-resolved photoelectron spectroscopies

Strocov, V.N. — 2010-09-01

The concepts and technical realisation of the high-resolution soft X-ray beamline ADRESS operating in the energy range from 300 to 1600 eV and intended for resonant inelastic X-ray scattering (RIXS) and angle-resolved photoelectron spectroscopy (ARPES) are described. The photon source is an undulator of novel fixed-gap design where longitudinal movement of permanent magnetic arrays controls not only the light polarization (including circular and 0–180° rotatable linear polarizations) but also the energy without changing the gap. The beamline optics is based on the well established scheme of plane-grating monochromator operating in collimated light. The ultimate resolving power E/ΔE is above 33000 at 1 keV photon energy. The choice of blazed versus lamellar gratings and optimization of their profile parameters is described. Owing to glancing angles on the mirrors as well as optimized groove densities and profiles of the gratings, the beamline is capable of delivering high photon flux up to 1 × 1013 photons s−1 (0.01% BW)−1 at 1 keV. Ellipsoidal refocusing optics used for the RIXS endstation demagnifies the vertical spot size down to 4 µm, which allows slitless operation and thus maximal transmission of the high-resolution RIXS spectrometer delivering E/ΔE > 11000 at 1 keV photon energy. Apart from the beamline optics, an overview of the control system is given, the diagnostics and software tools are described, and strategies used for the optical alignment are discussed. An introduction to the concepts and instrumental realisation of the ARPES and RIXS endstations is given.

Radiation dose optimized lateral expansion of the field of view in synchrotron radiation X-ray tomographic microscopy

Haberthür, D. — 2010-09-01

Volumetric data at micrometer level resolution can be acquired within a few minutes using synchrotron-radiation-based tomographic microscopy. The field of view along the rotation axis of the sample can easily be increased by stacking several tomograms, allowing the investigation of long and thin objects at high resolution. On the contrary, an extension of the field of view in the perpendicular direction is non-trivial. This paper presents an acquisition protocol which increases the field of view of the tomographic dataset perpendicular to its rotation axis. The acquisition protocol can be tuned as a function of the reconstruction quality and scanning time. Since the scanning time is proportional to the radiation dose imparted to the sample, this method can be used to increase the field of view of tomographic microscopy instruments while optimizing the radiation dose for radiation-sensitive samples and keeping the quality of the tomographic dataset on the required level. This approach, dubbed wide-field synchrotron radiation tomographic microscopy, can increase the lateral field of view up to five times. The method has been successfully applied for the three-dimensional imaging of entire rat lung acini with a diameter of 4.1 mm at a voxel size of 1.48 µm.

X-ray reflectivity theory for determining the density profile of a liquid under nanometre confinement

Perret, E. — 2010-07-01

An X-ray reflectivity theory on the determination of the density profile of a molecular liquid under nanometre confinement is presented. The confinement geometry acts like an X-ray interferometer, which consists of two opposing atomically flat single-crystal mica membranes with an intervening thin liquid film of variable thickness. The X-rays reflected from the parallel crystal planes (of known structure) and the layered liquid in between them (of unknown structure) interfere with one another, making X-ray reflectivity highly sensitive to the liquid's density profile along the confinement direction. An expression for the reflected intensity as a function of momentum transfer is given. The total structure factor intensity for the liquid-filled confinement device is derived as a sum of contributions from the inner and outer crystal terminations. The method presented readily distinguishes the confined liquid from the liquid adsorbed on the outer mica surfaces. It is illustrated for the molecular liquid tetrakis(trimethyl)siloxysilane, confined by two mica surfaces at a distance of 8.6 nm.

Quantification of phosphorus in single cells using synchrotron X-ray fluorescence

Núñez-Milland, D.R. — 2010-07-01

Phosphorus is required for numerous cellular compounds and as a result can serve as a useful proxy for total cell biomass in studies of cell elemental composition. Single-cell analysis by synchrotron X-ray fluorescence (SXRF) enables quantitative and qualitative analyses of cell elemental composition with high elemental sensitivity. Element standards are required to convert measured X-ray fluorescence intensities into element concentrations, but few appropriate standards are available, particularly for the biologically important element P. Empirical P conversion factors derived from other elements contained in certified thin-film standards were used to quantify P in the model diatom Thalassiosira pseudonana, and the measured cell quotas were compared with those measured in bulk by spectrophotometry. The mean cellular P quotas quantified with SXRF for cells on Au, Ni and nylon grids using this approach were not significantly different from each other or from those measured spectrophotometrically. Inter-cell variability typical of cell populations was observed. Additionally, the grid substrates were compared for their suitability to P quantification based on the potential for spectral interferences with P. Nylon grids were found to have the lowest background concentrations and limits of detection for P, while background concentrations in Ni and Au grids were 1.8- and 6.3-fold higher. The advantages and disadvantages of each grid type for elemental analysis of individual phytoplankton cells are discussed.

Current events

2010-05-01

Simultaneous measurement of X-ray specular reflection and off-specular diffuse scattering from liquid surfaces using a two-dimensional pixel array detector: the liquid-interface reflectometer of BL37XU at SPring-8

Yano, Y.F. — 2010-07-01

An X-ray reflectometer for simultaneous measurement of specular and off-specular reflection of liquid surfaces is described. The reflectometer, equipped with a two-dimensional single X-ray photon-counting pixel array detector obtained the full range of X-ray specular and off-specular reflections in an extremely short time (1 s). Both the specular and off-specular reflection of water exhibited good agreement with the predicted capillary-wave theory within the appropriate instrumental resolution. The approach is also demonstrated on an aqueous solution of 1-dodecyl-3-methylimidazolium chloride. The monolayer in which the dodecyl chain faces upwards and the Cl− anion locates next to the imidazolium ring formed on the water surface was found to be laterally homogeneous. The use of a pixel array detector will be particularly powerful for in situ measurements to investigate both out-of-plane and in-plane structures simultaneously, not only for liquid surfaces but also for other thin films.

Impact of synchrotron radiation on macromolecular crystallography: a personal view

Dauter, Z. — 2010-07-01

The introduction of synchrotron radiation sources almost four decades ago has led to a revolutionary change in the way that diffraction data from macromolecular crystals are being collected. Here a brief history of the development of methodologies that took advantage of the availability of synchrotron sources are presented, and some personal experiences with the utilization of synchrotrons in the early days are recalled.

Wavelength-dispersive spectrometer for X-ray microfluorescence analysis at the X-ray microscopy beamline ID21 (ESRF)

Szlachetko, J. — 2010-05-01

The development of a wavelength-dispersive spectrometer for microfluorescence analysis at the X-ray Microscopy ID21 beamline of the European Synchrotron Radiation Facility (ESRF) is reported. The spectrometer is based on a polycapillary optic for X-ray fluorescence collection and is operated in a flat-crystal geometry. The design considerations as well as operation characteristics of the spectrometer are presented. The achieved performances, in particular the energy resolution, are compared with the results of Monte Carlo simulations. Further improvement in the energy resolution, down to ∼eV range, by employing a double-crystal geometry is examined. Finally, examples of applications requiring both spatial and spectral resolutions are presented.

European Synchrotron User Organization established

Pietsch, U. — 2010-05-01

A report on the establishment of the European Synchrotron User Organization (ESUO), a body representing the interests of synchrotron radiation users across Europe.

Density measurement of samples under high pressure using synchrotron microtomography and diamond anvil cell techniques

Xiao, X. — 2010-05-01

Accurate mass density information is critical in high-pressure studies of materials. It is, however, very difficult to measure the mass densities of amorphous materials under high pressure with a diamond anvil cell (DAC). Employing tomography to measure mass density of amorphous samples under high pressure in a DAC has recently been reported. In reality, the tomography data of a sample in a DAC suffers from not only noise but also from the missing angle problem owing to the geometry of the DAC. An algorithm that can suppress noise and overcome the missing angle problem has been developed to obtain accurate mass density information from such ill-posed data. The validity of the proposed methods was supported with simulations.

In vivo pink-beam imaging and fast alignment procedure for rat brain lesion microbeam radiation therapy

Serduc, R. — 2010-05-01

A fast 50 µm-accuracy alignment procedure has been developed for the radiosurgery of brain lesions in rats, using microbeam radiation therapy. In vivo imaging was performed using the pink beam (35–60 keV) produced by the ID17 wiggler at the ESRF opened at 120 mm and filtered. A graphical user interface has been developed in order to define the irradiation field size and to position the target with respect to the skull structures observed in X-ray images. The method proposed here allows tremendous time saving by skipping the swap from white beam to monochromatic beam and vice versa. To validate the concept, the somatosensory cortex or thalamus of GAERS rats were irradiated under several ports using this alignment procedure. The magnetic resonance images acquired after contrast agent injection showed that the irradiations were selectively performed in these two expected brain regions. Image-guided microbeam irradiations have therefore been realised for the first time ever, and, thanks to this new development, the ID17 biomedical beamline provides a major tool allowing brain radiosurgery trials on animal patients.

X-ray magnetic circular dichroism measurements using an X-ray phase retarder on the BM25 A-SpLine beamline at the ESRF

Boada, R. — 2010-05-01

Circularly polarized X-rays produced by a diamond X-ray phase retarder of thickness 0.5 mm in the Laue transmission configuration have been used for recording X-ray magnetic circular dichroism (XMCD) on the bending-magnet beamline BM25A (SpLine) at the ESRF. Field reversal and helicity reversal techniques have been used to carry out the measurements. The performance of the experimental set-up has been demonstrated by recording XMCD in the energy range from 7 to 11 keV.

Current events

2010-03-01

Silicon saw-tooth refractive lens for high-energy X-rays made using a diamond saw

Said, A.H. — 2010-05-01

Silicon is a material well suited for refractive lenses operating at high X-ray energies (>50 keV), particularly if implemented in a single-crystal form to minimize small-angle scattering. A single-crystal silicon saw-tooth refractive lens, fabricated by a dicing process using a thin diamond wheel, was tested with 115 keV X-rays, giving an ideal 17 µm line focus width in a long focal length, 2:1 ratio demagnification geometry, with a source-to-focus distance of 58.5 m. The fabrication is simple, using resources typically available at any synchrotron facility's optics shop.

Synchrotron radiation in soil and geosciences

Terzano, R. — 2010-03-01

This special issue is the outcome of the Session SSS24 `Synchrotron radiation in soil and geosciences' that was held on 21 April 2009 in Vienna during the EGU (European Geosciences Union) General Assembly 2009, within the Soil System Sciences (SSS) program. In this special issue ten papers are presented, chosen after a selection among 19 written contributions that were received after the scientific Session at EGU.

In vitro synchrotron-based radiography of micro-gap formation at the implant–abutment interface of two-piece dental implants

Rack, A. — 2010-03-01

Micro-gap formation at the implant–abutment interface of two-piece dental implants was investigated in vitro using high-resolution radiography in combination with hard X-ray synchrotron radiation. Images were taken with the specimen under different mechanical loads of up to 100 N. The aim of this investigation was to prove the existence of micro-gaps for implants with conical connections as well as to study the mechanical behavior of the mating zone of conical implants during loading. Synchrotron-based radiography in comparison with classical laboratory radiography yields high spatial resolution in combination with high contrast even when exploiting micro-sized features in highly attenuating objects. The first illustration of a micro-gap which was previously indistinguishable by laboratory methods underlines that the complex micro-mechanical behavior of implants requires further in vitro investigations where synchrotron-based micro-imaging is one of the prerequisites.

Synchrotron radiation computed laminography for polymer composite failure studies

Xu, F. — 2010-03-01

Synchrotron radiation computed laminography is applied to the three-dimensional micro-imaging of damage in large polymer composite plates with high spatial resolution. The influence of different experimental conditions is studied with respect to measurement time optimization, dose minimization and reduction of artefacts in the reconstructed images. Failures like delaminations, transverse ply cracks and splits are observed under in situ loads. The propagation of up to 2 mm-long cracks is non-destructively followed in situ and investigated in detail. By phase retrieval using a single detector distance, the failures can be easily visualized in three dimensions.

Current events

2010-01-01

Development of a differential pumping system for soft X-ray beamlines for windowless experiments under normal atmospheric conditions

Tamenori, Y. — 2010-03-01

A novel design for a differential pumping system has been investigated. This system allows windowless experiments in a soft X-ray beamline under normal atmospheric conditions. The new design consists of an aperture-based four-stage differential pumping system, based on a simple model calculation. A prototype system with a total length of 600 mm was constructed to confirm the validity of the design concept. Relatively short conductance-limiting components allow easy installation and alignment of the system on a synchrotron beamline. The fabricated system was installed on a beamline to test the transmission of soft X-rays through atmospheric helium.

X-ray microdiffraction analysis of radiation-induced defects in single grains of polycrystalline Fe

Specht, E.D. — 2010-03-01

Single-crystal diffuse X-ray scattering was used to characterize radiation-induced defects in individual grains of a polycrystalline proton-irradiated Fe foil. The grains were probed with an intense 1 µm X-ray beam to demonstrate that both polycrystalline and micrometer-scale samples can be studied with single-crystal-like signal-to-noise. Scattering was measured with an X-ray-sensitive area detector, which measures intensity over a surface in reciprocal space. By scanning the X-ray energy, the intensity was measured over reciprocal-space volumes. Since the sample is not rotated, the real-space scattering volume does not change. Methods to minimize experimental artifacts arising from the use of an area detector are described.

X-ray spectroscopic approaches to the investigation and characterization of photochemical processes. Erratum

Kennepohl, P. — 2010-01-01

An error in the paper by Kennepohl et al. [(2009), J. Synchrotron Rad. 16, 484–488] is corrected.

Facing the challenge of biosample imaging by FTIR with a synchrotron radiation source

Petibois, C. — 2010-01-01

Fourier-transform infrared (FTIR) synchrotron radiation (SR) microspectroscopy is a powerful molecular probe of biological samples at cellular resolution (<10 µm). As the brilliance of SR is 100–1000 times higher than that of a conventional Globar source, FTIR microscopes are now available in almost all advanced SR facilities around the world. However, in spite of this superior performance, the expected advances in IR SR microscopy have not yet been realised, particularly with regard to bio-analytical studies of single cells and soft tissues. In recent decades solid-state array detectors have revolutionized the fields of molecular spectroscopy and chemical imaging, and now new IR focal plane array detectors implemented at ultra-bright SR facilities will extend the performance and overcome the existing limitations, possibly allowing IR SR instrumentation to achieve the highest sensitivity and resolution of molecular imaging. The impact of IR imaging on large tissue area and the complexity of the analysis are discussed. In view of the high brilliance of SR sources, a comparison of published microscope images is given. Finally, it is briefly outlined how an optimized combination of IR instrumentation and SR optical systems could reach the expected advantages of a SR-based FTIR imaging system.

Synchrotron-radiation-stimulated etching of polydimethylsiloxane using XeF2 as a reaction gas

Chiang, T.-Y. — 2010-01-01

The synchrotron radiation (SR) stimulated etching of silicon elastomer polydimethylsiloxane (PDMS) using XeF2 as an etching gas has been demonstrated. An etching system with differential pumps and two parabolic focusing mirrors was constructed to perform the etching. The PDMS was found to be effectively etched by the SR irradiation under the XeF2 gas flow, and the etching process was area-selective and anisotropic. An extremely high etching rate of 40–50 µm (10 min)−1 was easily obtained at an XeF2 gas pressure of 0.2–0.4 torr. This suggests that SR etching using XeF2 gas provides a new microfabrication technology for thick PDMS membranes, which can open new applications such as the formation of three-dimensional microfluidic circuits.

Temperature gradient analyzers for compact high-resolution X-ray spectrometers

Ishikawa, D. — 2010-01-01

Compact high-resolution X-ray spectrometers with a one-dimensional temperature gradient at the analyzer crystal are considered. This gradient, combined with the use of a position-sensitive detector, makes it possible to relax the usual Rowland-circle condition, allowing increased space at the sample position for a given energy resolution or arm radius. Thus, for example, it is estimated that ∼meV resolution is possible with a 3 m analyzer arm and 200 mm clearance between the sample and detector. Simple analytic formulae are provided, supported by excellent agreement with ray-tracing simulations. One variation of this method also allows the detector position sensitivity to be used to determine momentum transfer, effectively improving momentum resolution without reducing (slitting down) the analyzer size. Application to medium-resolution (∼10–100 meV) inelastic X-ray scattering spectrometers with large angular acceptance is discussed, where this method also allows increased space at the sample. In some cases the application of a temperature gradient can improve the energy resolution even with a single-element detector.

Current events

2009-11-01

Advances and synergy of high-pressure sciences at synchrotron sources

Liu, H. — 2009-11-01

Introductory overview to the special issue papers on high-pressure sciences and synchrotron radiation.

The ID23-2 structural biology microfocus beamline at the ESRF

Flot, D. — 2010-01-01

The first phase of the ESRF beamline ID23 to be constructed was ID23-1, a tunable MAD-capable beamline which opened to users in early 2004. The second phase of the beamline to be constructed is ID23-2, a monochromatic microfocus beamline dedicated to macromolecular crystallography experiments. Beamline ID23-2 makes use of well characterized optical elements: a single-bounce silicon (111) monochromator and two mirrors in Kirkpatrick–Baez geometry to focus the X-ray beam. A major design goal of the ID23-2 beamline is to provide a reliable, easy-to-use and routine microfocus beam. ID23-2 started operation in November 2005, as the first beamline dedicated to microfocus macromolecular crystallography. The beamline has taken the standard automated ESRF macromolecular crystallography environment (both hardware and software), allowing users of ID23-2 to be rapidly familiar with the microfocus environment. This paper describes the beamline design, the special considerations taken into account given the microfocus beam, and summarizes the results of the first years of the beamline operation.

Use of a hexapod in diffraction measurements of substrate-supported crystals of organic semiconductors

Yang, L. — 2009-11-01

Thin films of organic semiconductor prepared on substrates generally contain crystals that have one common crystal plane parallel to the substrate but random in-plane orientations. In diffraction measurements of these structures, it is often required to anchor the X-ray beam on a fixed spot on the sample, such as an optically visible crystallite or island. Here, a hexapod is used in place of a traditional multi-circle diffractometer to perform area-detector-based diffraction measurements on an actual device that contains 6,13-bis(triisopropylsilyethynyl)-pentacene (TIPS-pentacene) crystals. The hexapod allows for sample rotations about any user-defined rotation center. Two types of complex sample motions have been programmed to characterize the structure of the TIPS-pentacene crystal: an in-plane powder average has been performed at a fixed grazing-incident angle to determine the lattice parameters of the crystal; then the in-plane component of the scattering vector was continuously rotated in transmission geometry to determine the local crystal orientation.

A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

McCarthy, A.A. — 2009-11-01

ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade.

Current events

2009-09-01

Comments on Determination of X-ray flux using silicon pin diodes by R. L. Owen et al. (2009). J. Synchrotron Rad. 16, 143–151

Krumrey, M. — 2009-09-01

Response to Krumrey's Comments on Determination of X-ray flux using silicon pin diodes by R. L. Owen et al. (2009). J. Synchrotron Rad. 16, 143–153

Owen, R.L. — 2009-09-01

Current events

2009-07-01

Current events

2009-05-01

Performance of single-photon-counting PILATUS detector modules

Kraft, P. — 2009-05-01

PILATUS is a silicon hybrid pixel detector system, operating in single-photon-counting mode, that has been developed at the Paul Scherrer Institut for the needs of macromolecular crystallography at the Swiss Light Source (SLS). A calibrated PILATUS module has been characterized with monochromatic synchrotron radiation. The influence of charge sharing on the count rate and the overall energy resolution of the detector were investigated. The dead-time of the system was determined using the attenuated direct synchrotron beam. A single module detector was also tested in surface diffraction experiments at the SLS, whereby its performance regarding fluorescence suppression and saturation tolerance were evaluated, and have shown to greatly improve the sensitivity, reliability and speed of surface diffraction data acquisition.

X-ray diffractometry for the structure determination of a submicrometre single powder grain

Yasuda, N. — 2009-05-01

A high-precision diffractometer has been developed for the structure analysis of a submicrometre-scale single grain of a powder sample at the SPring-8 BL40XU undulator beamline. The key design concept is the combination of a stable focused synchrotron radiation beam and the precise axis control of the diffractometer, which allows accurate diffraction intensity data of a submicrometre-scale single powder grain to be measured. The phase zone plate was designed to create a high-flux focused synchrotron radiation beam. A low-eccentric goniometer and high-precision sample positioning stages were adopted to ensure the alignment of a micrometre-scale focused synchrotron radiation beam onto the submicrometre-scale single powder grain. In order to verify the diffractometer performance, the diffraction pattern data of several powder grains of BaTiO3, of dimensions ∼600 × 600 × 300 nm, were measured. By identifying the diffraction data set of one single powder grain, the crystal structure was successfully determined with a reliable factor of 5.24%.

100 ps time-resolved solution scattering utilizing a wide-bandwidth X-ray beam from multilayer optics

Ichiyanagi, K. — 2009-05-01

100 ps time-resolved X-ray solution-scattering capabilities have been developed using multilayer optics at the beamline NW14A, Photon Factory Advanced Ring, KEK. X-ray pulses with an energy bandwidth of ΔE/E = 1–5% are generated by reflecting X-ray pulses (ΔE/E = 15%) through multilayer optics, made of W/B4C or depth-graded Ru/C on silicon substrate. This tailor-made wide-bandwidth X-ray pulse provides high-quality solution-scattering data for obtaining photo-induced molecular reaction dynamics. The time-resolved solution scattering of CH2I2 in methanol is demonstrated as a typical example.

Comments on Migration of mercury from dental amalgam through human teeth by H. H. Harris et al. (2008). J. Synchrotron Rad. 15, 123–128

Guzzi, G. — 2009-05-01

Radiation damage in protein crystals examined under various conditions by different methods

Garman, E.F. — 2009-03-01

Investigation of radiation damage in protein crystals has progressed in several directions over the past couple of years. There have been improvements in the basic procedures such as calibration of the incident X-ray intensity and calculation of the dose likely to be deposited in a crystal of known size and composition with this intensity. There has been increased emphasis on using additional techniques such as optical, Raman or X-ray spectroscopy to complement X-ray diffraction. Apparent discrepancies between the results of different techniques can be explained by the fact that they are sensitive to different length scales or to changes in the electronic state rather than to movement of atoms. Investigations have been carried out at room temperature as well as cryo-temperatures and, in both cases, with the introduction of potential scavenger molecules. These and other studies are leading to an overall description of the changes which can occur when a protein crystal is irradiated with X-rays at both cryo- and room temperatures. Results from crystallographic and spectroscopic radiation-damage experiments can be reconciled with other studies in the field of radiation physics and chemistry.

A beginner's guide to radiation damage

Holton, J.M. — 2009-03-01

Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to radiation damage issues, and to provide references to the more exacting and detailed work. No attempt has been made to report precise numbers (a factor of two is considered satisfactory), and, since there are aspects of radiation damage that are demonstrably unpredictable, the `worst case scenario' as well as the `average crystal' are discussed in terms of the practicalities of data collection.

Classification of Fe-bearing species from K-edge XANES data using two-parameter correlation plots. Erratum

Marcus, M.A. — 2009-05-01

In the paper by Marcus et al. [(2008), J. Synchrotron Rad. 15, 463–468], an incorrect version of Table 1 was published. The correct version is given here.

Response to Guzzi & Pigatto's Comments on Migration of mercury from dental amalgam through human teeth by H. H. Harris et al. (2008). J. Synchrotron Rad. 15, 123–128

Harris, H.H. — 2009-05-01

Synchrotron-based radioscopy employing spatio-temporal micro-resolution for studying fast phenomena in liquid metal foams

Rack, A. — 2009-05-01

Investigations of pore coalescence and individual cell wall collapse in an expanding liquid metal foam by means of X-ray radioscopy with spatio-temporal micro-resolution are reported. By using white synchrotron radiation for imaging, the rupture of a film and the subsequent merger of two neighbouring bubbles could be recorded with a time sampling rate of 40000 frames s−1 (25 µs exposure time) and a spatial sampling rate of 20 µm. The rupture time of a cell wall was found to be in the range of 300 µs. This value is in agreement with theoretical considerations which assume an inertia-dominated rupture time of cell walls in liquid metal foams.

Colouring cryo-cooled crystals: online microspectrophotometry

McGeehan, J. — 2009-03-01

X-rays can produce a high concentration of radicals within cryo-cooled macromolecular crystals. Some radicals have large extinction coefficients in the visible (VIS) range of the electromagnetic spectrum, and can be observed optically and spectrally. An online microspectrophotometer with high temporal resolution has been constructed that is capable of measuring UV/VIS absorption spectra (200–1100 nm) during X-ray data collection. The typical X-ray-induced blue colour that is characteristic of a wide range of cryo-conditions has been identified as trapped solvated electrons. Disulphide-containing proteins are shown to form disulphide radicals at millimolar concentrations, with absorption maxima around 400 nm. The solvated electrons and the disulphide radicals seem to have a lifetime in the range of seconds up to minutes at 100 K. The temperature dependence of the kinetics of X-ray-induced radical formation is different for the solvated electrons compared with the disulphide radicals. The online microspectrophotometer provides a technique complementary to X-ray diffraction for analysing and characterizing intermediates and redox states of proteins and enzymes.

Current events

2009-01-01

Current events

2009-03-01

A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source

Owen, R.L. — 2009-03-01

X-ray crystallography at third-generation synchrotron sources permits tremendous insight into the three-dimensional structure of macromolecules. Additional information is, however, often required to aid the transition from structure to function. In situ spectroscopic methods such as UV–Vis absorption and (resonance) Raman can provide this, and can also provide a means of detecting X-ray-induced changes. Here, preliminary results are introduced from an on-axis UV–Vis absorption and Raman multimode spectrometer currently being integrated into the beamline environment at X10SA of the Swiss Light Source. The continuing development of the spectrometer is also outlined.

Determination of X-ray flux using silicon pin diodes

Owen, R.L. — 2009-03-01

Accurate measurement of photon flux from an X-ray source, a parameter required to calculate the dose absorbed by the sample, is not yet routinely available at macromolecular crystallography beamlines. The development of a model for determining the photon flux incident on pin diodes is described here, and has been tested on the macromolecular crystallography beamlines at both the Swiss Light Source, Villigen, Switzerland, and the Advanced Light Source, Berkeley, USA, at energies between 4 and 18 keV. These experiments have shown that a simple model based on energy deposition in silicon is sufficient for determining the flux incident on high-quality silicon pin diodes. The derivation and validation of this model is presented, and a web-based tool for the use of the macromolecular crystallography and wider synchrotron community is introduced.

Capturing molecular structural dynamics by 100 ps time-resolved X-ray absorption spectroscopy

Sato, T. — 2009-01-01

An experimental set-up for time-resolved X-ray absorption spectroscopy with 100 ps time resolution at beamline NW14A at the Photon Factory Advanced Ring is presented. The X-ray positional active feedback to crystals in a monochromator combined with a figure-of-merit scan of the laser beam position has been utilized as an essential tool to stabilize the spatial overlap of the X-ray and laser beams at the sample position. As a typical example, a time-resolved XAFS measurement of a photo-induced spin crossover reaction of the tris(1,10-phenanthrorine)iron(II) complex in water is presented.

Current events

2008-11-01

Current events

2008-09-01

PI-MTE cameras now twice as fast with 2 MHz readout

Flint-Baum, D. — 2008-09-01

A coherent synchrotron X-ray microradiology investigation of bubble and droplet coalescence

Weon, B.M. — 2008-11-01

A quantitative application of microradiology with coherent X-rays to the real-time study of microbubble and microdroplet coalescence phenomena, with specific emphasis on the size relations in three-body events, is presented. The results illustrate the remarkable effectiveness of coherent X-ray imaging in delineating interfaces in multiphase systems, in accurately measuring their geometric properties and in monitoring their dynamics.

Current events

2008-07-01

Current events

2008-05-01

Development of an X-ray HARP–FEA detector system for high-throughput protein crystallography

Miyoshi, T. — 2008-05-01

A new detector system for protein crystallography is now being developed based on an X-ray HARP–FEA (high-gain avalanche rushing amorphous photoconductor–field emitter array), which consists of an amorphous selenium membrane and a matrix field emitter array. The combination of the membrane avalanche effect with a single driven FEA has several advantages over currently available area detectors, including higher sensitivity, higher spatial resolution and a higher frame rate. Preliminary evaluation of the detector has been carried out and its effectiveness has been confirmed. Next, diffraction images were measured with continuous rotation of a protein crystal, and the images were compared with those measured by the existing CCD detector; the system successfully obtained high-spatial-resolution images. Using shutterless measurement, the total measurement time can be reduced significantly, making the method appropriate for high-throughput protein crystallography. The X-ray HARP–FEA detector is an attractive candidate for the next generation of X-ray area detectors.

Structure of six-transmembrane cation channels revealed by single-particle analysis from electron microscopic images

Mio, K. — 2008-05-01

Six-transmembrane (6-TM) cation channels are plasma membrane-integral components of cellular signaling pathways conserved in almost all species, including animals, plants and some kinds of prokaryotes. These channels selectively permeate cations in response to various signals. In excitable and non-excitable mammalian cells, 6-TM cation channels play fundamental roles, including the generation of action potential and its transmission, the regulation of intracellular ion concentrations, and the activation of signaling cascades by humoral or mechanical pathways. Recently, the structures of three different 6-TM-type cation channels have been determined using single-particle analysis from cryo-electron microscopy images: the voltage-sensitive sodium channel, the IP3 receptor and the TRPC3 channel. The basic structure of the molecules is similar: a bell-like shape comprising a relatively small extracellular (or luminal) domain, a protein-dense transmembrane domain and an expanded cytoplasmic domain. However, in detail, the cytoplasmic architectures are different from one another and are diversely evolved to their specific physiological functions.

Mutagenesis of the crystal contact of acidic fibroblast growth factor

Honjo, E. — 2008-05-01

An attempt has been made to improve a crystal contact of human acidic fibroblast growth factor (haFGF; 140 amino acids) to control the crystal growth, because haFGF crystallizes only as a thin-plate form, yielding crystals suitable for X-ray but not neutron diffraction. X-ray crystal analysis of haFGF showed that the Glu81 side chain, located at a crystal contact between haFGF molecules, is in close proximity with an identical residue related by crystallographic symmetry, suggesting that charge repulsion may disrupt suitable crystal-packing interactions. To investigate whether the Glu residue affects the crystal-packing interactions, haFGF mutants in which Glu81 was replaced by Ala, Val, Leu, Ser and Thr were constructed. Although crystals of the Ala and Leu mutants were grown as a thin-plate form by the same precipitant (formate) as the wild type, crystals of the Ser and Thr mutants were grown with increased thickness, yielding a larger overall crystal volume. X-ray structural analysis of the Ser mutant determined at 1.35 Å resolution revealed that the hydroxy groups of Ser are linked by hydrogen bonds mediated by the formate used as a precipitant. This approach to engineering crystal contacts may contribute to the development of large protein crystals for neutron crystallography.

Current events

2008-03-01

Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines

Yamada, Y. — 2008-05-01

Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client–server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system.

Highly bright X-ray generator using heat of fusion with a specially designed rotating anticathode

Sakabe, N. — 2008-05-01

A new type of rotating anticathode X-ray generator has been developed, in which the electron beam irradiates the inner surface of a U-shaped anticathode (Cu). A high-flux electron beam is focused on the inner surface by optimizing the shape of the bending magnet. The power of the electron beam can be increased to the point at which the irradiated part of the inner surface is melted, because a strong centrifugal force fixes the melted part on the inner surface. When the irradiated part is melted, a large amount of energy is stored as the heat of fusion, resulting in emission of X-rays 4.3 times more brilliant than can be attained by a conventional rotating anticathode. Oscillating translation of the irradiated position on the inner surface during use is expected to be very advantageous for extending the target life. A carbon film coating on the inner surface is considered to suppress evaporation of the target metal and will be an important technique in further realization of highly bright X-ray generation.

High-resolution X-ray microdiffraction analysis of natural teeth

Xue, J. — 2008-05-01

The main component of natural teeth was determined many years ago as calcium phosphate, mostly in the form of hydroxyapatite with different crystallites. In the past, the method used in tooth crystal investigation has been mainly powder X-ray diffraction analysis, but this method has its drawbacks, i.e. the destruction of the natural tooth structure and the difficulty in examining the preferred orientation in different layers of the tooth. During the last century, microzone X-ray diffraction on the tooth surface was carried out, but, as the technology was less sophisticated, the results obtained were not very detailed. The newly developed microdiffraction equipment permits analysis of the microzone of teeth in situ. To test this new microdiffraction equipment, microdiffraction analysis of one natural healthy deciduous molar tooth and one carious deciduous molar tooth has been performed, using a Bruker D8 instrument. Phase analysis of the two teeth was performed; the crystal size at six test points in the natural healthy tooth was calculated by reflection (211), and the crystal preferred orientation of reflection (300) and reflection (002) at six test points in the natural healthy tooth were compared. The results showed that the tooth was a kind of biological mixed crystal composed of several crystal phases, the main crystal phase being hydroxyapatite. The crystal size grew larger going from the dentin to the enamel. The crystal preferred orientation mainly existed in the enamel, especially in the reflection (002). From our experiment, layer orientation and continuous crystal variations in teeth could be conveniently studied using fast online measurements by high-resolution X-ray microdiffraction equipment.

X-ray crystallographic and biochemical characterizations of a mutant photosystem II complex from Thermosynechococcus vulcanus with the psbTc gene inactivated by an insertion mutation

Henmi, T. — 2008-05-01

The crystal structure of a photosystem II (PSII) dimer from Thermosynechococcus vulcanus with its psbTc gene inactivated by insertion mutation of an antibiotic cassette in a site in the C-terminal region was analyzed at 3.8 Å resolution. In the crystal structure of the mutant PSII, the transmembrane helix of PsbTc remains, whereas the C-terminal loop of PsbTc has disappeared. In addition, the PsbM subunit, which seemed to be lost in a PsbTc-deletion mutant PSII of T. elongatus, is still present. The deletion of the C-terminal loop of PsbTc in the mutant PSII was verified by mass spectrometry. Thus, the insertion mutation of psbTc eliminated only the C-terminal loop of this subunit. Nevertheless, some features of the mutant PSII, namely a destabilization of the dimeric form and a slight decrease of the oxygen-evolving activity, were observed in the mutant, indicating that the C-terminal loop of PsbTc functions to maintain the stability of the PSII dimer and the activity of oxygen evolution.

Protein crystallization in a 100 nl solution with new stirring equipment

Maki, S. — 2008-05-01

To investigate quantitatively the effects of stirring on protein crystallization, a new stirring system which can agitate a protein solution, ∼100 nl, by providing Hagen–Poiseuille flow has been successfully developed. In addition, this new stirring system provides flow with a well defined pattern and velocity. Using this system, hen egg-white lysozyme was crystallized in 100–200 nl solutions while being stirred. The optimum stirring conditions for lysozyme crystals have been explored by evaluating the Reynolds (Re) number and the crystals obtained. Intermittent flow, as well as a low Re number, was found to contribute significantly to the growth of a smaller number of larger crystals.

Protein structures by spallation neutron crystallography

Langan, P. — 2008-05-01

The Protein Crystallography Station at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University.

Structural studies on Helicobacter pylori ATP-dependent protease, FtsH

Kim, S.H. — 2008-05-01

The ATP-dependent protease, FtsH, degrades misassembled membrane proteins for quality control like SecY, subunit a of FoF1-ATPase, and YccA, and digests short-lived soluble proteins in order to control their cellular regulation, including σ32, LpxC and λcII. The FtsH protein has an N-terminal transmembrane segment and a large cytosolic region that consists of two domains, an ATPase and a protease domain. To provide a structural basis for the nucleotide-dependent domain motions and a better understanding of substrate translocation, the crystal structures of the Helicobacter pylori (Hp) FtsH ATPase domain in the nucleotide-free state and complexed with ADP, were determined. Two different structures of HpFtsH ATPase were observed, with the nucleotide-free state in an asymmetric unit, and these structures reveal the new forms and show other conformational differences between the nucleotide-free and ADP-bound state compared with previous structures. In particular, one HpFtsH Apo structure has a considerable rotation difference compared with the HpFtsH ADP complex, and this large conformational change reveals that FtsH may have the mechanical force needed for substrate translocation.

Science experiments via telepresence at a synchrotron radiation source facility

Warren, J.E. — 2008-03-01

Station 9.8 is one of the most oversubscribed and high-throughput stations at the Synchrotron Radiation Source, Daresbury, whereby awarded experimental time is limited, data collections last normally no longer than an hour, user changeover is normally every 24 h, and familiarity with the station systems can be low. Therefore time lost owing to technical failures on the station has a dramatic impact on productivity. To provide 24 h support, the application of a turnkey communication system has been implemented, and is described along with additional applications including its use for inter-continental classroom instruction, user training and remote participation.

Ultrahigh-resolution crystallography and related electron density and electrostatic properties in proteins

Lecomte, C. — 2008-05-01

With an increasing number of biological macromolecular crystal structures measured at ultrahigh resolution (1 Å or better), it is necessary to extend to large systems the experimental valence electron density modelling that is applied to small molecules. A database of average multipole populations has been built, describing the electron density of chemical groups in all 20 amino acids found in proteins. It allows calculation of atomic aspherical scattering factors, which are the starting point for refinement of the protein electron density, using the MoPro software. It is shown that the use of non-spherical scattering factors has a major impact on crystallographic statistics and results in a more accurate crystal structure, notably in terms of thermal displacement parameters and bond distances involving H atoms. It is also possible to obtain a realistic valence electron density model, which is used in the calculation of the electrostatic potential and energetic properties of proteins.

Effect of amino acids and amino acid derivatives on crystallization of hemoglobin and ribonuclease A

Ito, L. — 2008-05-01

Determination of the appropriate conditions for protein crystallization remains a highly empirical process. Preventing protein aggregation is necessary for the formation of single crystals under aggregation-prone solution conditions. Because many amino acids and amino acid derivatives offer a unique combination of solubility and stabilizing properties, they open new avenues into the field of protein aggregation research. The use of amino acids and amino acid derivatives can potentially influence processes such as heat treatment and refolding reactions. The effect of the addition of several amino acids, such as lysine, and several amino acid derivatives, such as glycine ethyl ester and glycine amide, on the crystallization of equine hemoglobin and bovine pancreatic ribonuclease A has been examined. The addition of these amino acids and amino acid derivatives expanded the range of precipitant concentration in which crystals formed without aggregation. The addition of such additives appears to promote the crystallization of proteins.

Interaction of HIV-1 aspartic protease with its inhibitor, by molecular dynamics and ab initio fragment molecular orbital method

Koyano, K. — 2008-05-01

For the three complex crystal structures of HIV-1 aspartic protease (an enzyme of AIDS) with its inhibitor in the Protein Data Bank, molecular dynamics of the generalized Born surface area and the ab initio fragment molecular orbital of an ABINIT-MP calculation was performed to obtain the binding free energy, the molecular orbital energy, the interaction energy of residues with an inhibitor and the charge transfer at the active site. The inhibitors are five symmetric cyclic ureas, of which three were modelled, and an asymmetric dipeptide. The interaction energy of the inhibitor at the active sites of aspartic acid is as great as 50 kcal mol−1, coinciding with a tetrahedral transition state. For the inhibitor with a higher affinity, charge was transferred to the inhibitor from the active site. The difference in symmetry of the inhibitor was not evident. Binding free energy corresponds to the experimental value of the binding constant, while molecular orbital energy does not always, which is considered to be an entropy effect.

Novel dimer structure of a membrane-bound protease with a catalytic Ser–Lys dyad and its linkage to stomatin

Yokoyama, H. — 2008-05-01

Membrane-bound proteases are involved in various regulatory functions. A previous report indicates that the N-terminal region of PH1510 (1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii is a serine protease with a catalytic Ser–Lys dyad (Ser97 and Lys138), and specifically cleaves the C-terminal hydrophobic region of the p-stomatin PH1511. According to the crystal structure of the wild-type 1510-N in dimeric form, the active site around Ser97 is in a hydrophobic environment suitable for the hydrophobic substrates. This article reports the crystal structure of the K138A mutant of 1510-N at 2.3 Å resolution. The determined structure contains one molecule per asymmetric unit, but 1510-N is active in dimeric form. Two possible sets of dimer were found from the symmetry-related molecules. One dimer is almost the same as the wild-type 1510-N. Another dimer is probably in an inactive form. The L2 loop, which is disordered in the wild-type structure, is significantly kinked at around A-138 in the K138A mutant. Thus Lys138 probably has an important role on the conformation of L2.

X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory

Igarashi, N. — 2008-05-01

BL-17A is a new structural biology beamline at the Photon Factory, Japan. The high-brilliance beam, derived from the new short-gap undulator (SGU#17), allows for unique protein crystallographic experiments such as data collection from microcrystals and structural determination using softer X-rays. However, microcrystal experiments require robust beam stability during data collection and minor fluctuations could not be ignored. Initially, significant beam instability was observed at BL-17A. The causes of the beam instability were investigated and its various sources identified. Subsequently, several effective countermeasures have been implemented, and the fluctuation of the beam intensity successfully suppressed to within 1%. Here the instability reduction techniques used at BL-17A are presented.

Performance of an electron gun for a high-brightness X-ray generator

Sugimura, T. — 2008-05-01

A prototype thermionic electron gun for a high-brightness X-ray generator has been developed. Its extraction voltage and design current are 60 kV and 100 mA (DC), respectively. The X-ray generator aims towards a maximum brilliance of 60 kW mm−2. The beam sizes at the rotating anticathode must therefore be within 1.0 mm × 0.1 mm and a small beam emittance is required. The fabricated electron gun optimizes an aperture grid and a Whenelt electrode. The performance of the prototype electron gun measured using pulsed-beam tests is as follows: maximum beam current, 85.7 mA; beam focus size at the rotating anticathode, 0.79 mm × 0.13 mm. In DC beam tests, FWHM beam sizes were measured to be 0.65 mm × 0.08 mm at the rotating anticathode with a beam current of 45 mA. The beam current recently reached ∼60 mA with some thermal problems.

Solution structures of RseA and its complex with RseB

Jin, K.S. — 2008-05-01

The bacterial envelope stress response, which is responsible for sensing stress signals in the envelope and for turning on the σE-dependent transcription, is modulated by the binding of RseB to RseA. In this study, the solution structures of RseA and its complex with RseB were analyzed using circular dichroism and small-angle X-ray scattering. The periplasmic domain of RseA is unstructured and flexible when it is not bound to RseB. However, upon the formation of the stable complex with RseB, RseA induces conformational changes in RseB and, at the same time, RseA becomes more structured. Furthermore, it appears that some other undefined region of RseA, as well as the previously identified minimum region (amino acid 169–186), is also involved in RseB binding. It is thought that these conformational changes are relevant to the proteolytic cleavage of RseA and the modulation of envelope stress response.

Current events

2008-01-01

Protein disulfide bond generation in Escherichia coli DsbB–DsbA

Inaba, K. — 2008-05-01

Protein disulfide bond formation is catalyzed by a series of Dsb enzymes present in the periplasm of Escherichia coli. The crystal structure of the DsbB–DsbA–ubiquinone ternary complex provided important insights into mechanisms of the de novo disulfide bond generation cooperated by DsbB and ubiquinone and of the disulfide bond shuttle from DsbB to DsbA. The structural basis for prevention of the crosstalk between the DsbA–DsbB oxidative and the DsbC–DsbD reductive pathways has also been proposed.

Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide

Ohto, U. — 2008-05-01

Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The cA axis of domain A coincides with the cB axis of domain B with a smaller lattice, and the aA axis corresponds to the (aB + bB) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P41212 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method.

Fragment approaches in structure-based drug discovery

Hubbard, R.E. — 2008-05-01

There has been considerable interest recently in what is known as `fragment-based lead discovery'. The novel feature of the approach is to begin with small low-affinity compounds. The main advantage is that a larger potential chemical diversity can be sampled with fewer compounds, which is particularly important for new target classes. The approach relies on careful design of the fragment library, a method that can detect binding of the fragment to the protein target, determination of the structure of the fragment bound to the target, and the conventional use of structural information to guide compound optimization. In this article the methods are reviewed, and experiences in fragment-based discovery of lead series of compounds against kinases such as PDK1 and ATPases such as Hsp90 are discussed. The examples illustrate some of the key benefits and issues of the approach and also provide anecdotal examples of the patterns seen in selectivity and the binding mode of fragments across different protein targets.

Mail-in data collection at SPring-8 protein crystallography beamlines

Okazaki, N. — 2008-05-01

A mail-in data collection system makes it possible for beamline users to collect diffraction data without visiting a synchrotron facility. In the mail-in data collection system at SPring-8, users pack crystals into sample trays and send the trays to SPring-8 via a courier service as the first step. Next, the user specifies measurement conditions and checks the diffraction images via the Internet. The user can also collect diffraction data using an automated sample changer robot and beamline control software. For distant users there is a newly developed data management system, D-Cha. D-Cha provides a graphical user interface that enables the user to specify the experimental conditions for samples and to check and download the diffraction images using a web browser. This system is now in routine operation and is contributing to high-throughput beamline operation.

An optimal exposure strategy for cryoprotected virus crystals with lattice constants greater than 1000 Å

Gan, L. — 2008-05-01

Studies of icosahedral virus capsids provide insights into the function of supramolecular machines. Virus capsid crystals have exceptionally large unit cells; as a result, they diffract weakly compared with protein crystals. HK97 is a dsDNA lambda-like bacteriophage whose 13 MDa capsid expands from 550 Å to 650 Å with large subunit conformational changes during virus maturation. The HK97 penultimate maturation intermediate was crystallized in a tetragonal unit cell that has lattice constants of 1010 Å × 1010 Å × 730 Å. The crystals could be cryoprotected, but diffracted to a modest resolution of 5 Å at a bending-magnet beamline. When these crystals were optimally exposed with two orders-of-magnitude more photons from a new insertion-device beamline, data extending to better than 3.8 Å resolution were obtained. Here, the strategies to collect and process such data are described. These strategies can be adapted for other crystals with large unit cells and for microcrystals.

High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines

Hiraki, M. — 2008-05-01

Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10 s.

Deduced catalytic mechanism of d-amino acid amidase from Ochrobactrum anthropi SV3

Okazaki, S. — 2008-05-01

d-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered Ω loop, and a ground state with a disordered Ω loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 Oη, Ser60 Oγ and Lys63 Nζ revealed that Tyr149 Oη donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 Oη donates an H atom to Ser60 Oγ or Lys63 Nζ in the ground state. Taking into consideration the locations of the H atoms of Tyr149 Oη, Ser60 Oγ and Lys63 Nζ, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 Oη in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state.

Key steps in the structure-based optimization of the hepatitis C virus NS3/4A protease inhibitor SCH503034

Madison, V. — 2008-05-01

The structures of both native and S139A holo-HCV NS3/4A protease domain were solved to high resolution. Subsequently, structures were determined for a series of ketoamide inhibitors in complex with the protease. The changes in the inhibitor potency were correlated with changes in the buried surface area upon binding the inhibitor to the active site. The largest contributions to the binding energy arise from the hydrophobic interactions of the P1 and P2 groups as they bind to the S1 and S2 pockets. This correlation of the changes in potency with increased buried surface area contributed directly to the design of a potent tripeptide inhibitor of the HCV NS3/4A protease, which is currently in clinical trials.

A degradation signal recognition in prokaryotes

Park, E.Y. — 2008-05-01

The degradation of ssrA-tagged substrates in prokaryotes is conducted by a subset of ATP-dependent proteases, including ClpXP complex. More than 630 sequences of ssrA have been identified from 514 species, and are conserved in a wide range of prokaryotes. SspB protein markedly stimulates the degradation of these ssrA-tagged substrates by the ClpXP proteolytic machine. The dimeric SspB protein is composed of a compact ssrA-binding domain, which has a dimerization surface and a flexible C-terminal tail with a ClpX-binding motif at its very end. Since SspB is an adaptor protein for the ClpXP complex, designed mutagenesis, fluorescence spectroscopy, biochemistry and X-ray crystallography have been used to investigate the mechanism of delivery of ssrA-tagged proteins. In this paper the structural basis of ssrA-tag recognition by ClpX and SspB, as well as SspB-tail recognition by ZBD, is described.

Complex of human neutrophil elastase with 1/2SLPI

Koizumi, M. — 2008-05-01

SLPI (secretory leukocyte protease inhibitor) is a 107-residue non-glycosylated protease inhibitor, which inhibits a wide range of serine proteases, trypsin, chymotrypsin, neutrophil elastase, chymase and cathepsin G. X-ray crystallographic analyses have shown that SLPI comprises two separate domains of similar architecture [Grütter, Fendrich, Huber & Bode (1988), EMBO J. 7, 345–351] and the C-terminal domain interacts with bovine α-chymotrypsin. In order to understand SLPI's multiple functions against various serine proteases, the complex HNE (human neutrophil elastase) has been co-crystallized with 1/2SLPI (recombinant C-terminal domain of SLPI; Arg58–Ala107), which has a biological activity similar to full SLPI. The 1/2SLPI and HNE complex structure was solved at 1.7 Å resolution, and compared with the interaction mechanism of elafin, which is a specific inhibitor of elastase. It was found that P1 Leu72i and six hydrogen bonds between the main chains in the primary contact region have sufficient ability to inhibit HNE and PPE (porcine pancreatic elastase), and P5 Tyr68i is important in increasing the selectivity of 1/2SLPI against HNE. The mechanisms of the functions of SLPI are relatively unknown, but the current study could help understand the selectivity of SLPI against HNE and PPE.

Crystallization and evaluation of hen egg-white lysozyme crystals for protein pH titration in the crystalline state

Iwai, W. — 2008-05-01

To observe the ionized status of the amino acid residues in proteins at different pH (protein pH titration in the crystalline state) by neutron diffraction, hen egg-white lysozyme was crystallized over a wide pH range (2.5–8.0). Crystallization phase diagrams at pH 2.5, 6.0 and 7.5 were determined. At pH < 4.5 the border between the metastable region and the nucleation region shifted to the left (lower precipitant concentration) in the phase diagram, and at pH > 4.5 the border shifted to the right (higher precipitant concentration). The qualities of these crystals were characterized using the Wilson plot method. The qualities of all crystals at different pH were more or less equivalent (B-factor values within 25–40). It is expected that neutron diffraction analysis of these crystals of different pH provides equivalent data in quality for discussions of protein pH titration in the crystalline state of hen egg-white lysozyme.

Hydrogen bonds of DsrD protein revealed by neutron crystallography

Chatake, T. — 2008-05-01

The features of hydrogen bonds in DsrD protein from sulfate-reducing bacteria have been investigated by neutron protein crystallography. The function of DsrD has not yet been elucidated clearly, but its X-ray crystal structure revealed that it comprises a winged-helix motif and shows the highest structural homology to the DNA-binding proteins. Since any neutron structure of a DNA recognition protein has not yet been obtained, here detailed information on the hydrogen bonds in the winged-helix-motif protein is given and the following features found. (i) The number of hydrogen bonds per amino acid of DsrD is relatively fewer than for other proteins for which neutron structures were determined previously. (ii) Hydrogen bonds are localized between main-chain and main-chain atoms; there are few hydrogen bonds between main-chain and side-chain atoms and between side-chain and side-chain atoms. (iii) Hydrogen bonds inducted by protonation of specific amino acid residues (Glu50) seem to play an essential role in the dimerization of DsrD. The former two points are related to the function of the DNA-binding protein; the three-dimensional structure was mainly constructed by hydrogen bonds in main chains, while the side chains appeared to be used for another role. The latter point would be expected to contribute to the crystal growth of DsrD.

Cost-effective upgrade of a focusing system for inelastic X-ray scattering experiments under high pressure

Huang, C.-Y. — 2008-01-01

Inelastic X-ray scattering (IXS) is a powerful technique capable of probing the dynamic behavior and electronic structure of materials. For IXS experiments under high pressure up to the megabar range using state-of-the-art diamond-anvil-cell technology, the sample volume is limited to the order of 1 × 10−3 mm3 for which a beam focus of the same order and less is often required. In this paper a scheme utilizing a set of low-cost and compact Kirkpatrick–Baez mirrors for upgrading the existing optical system of the Taiwan IXS beamline at SPring-8 is described. The scheme as implemented improves the focus to 13 µm × 16 µm (horizontal × vertical) with a transmission of up to 72% and a flux density gain of over 30 times, which has enhanced substantially the efficiency of the beamline for high-pressure research.

Crystallization of the Atg12–Atg5 conjugate bound to Atg16 by the free-interface diffusion method

Noda, N.N. — 2008-05-01

Autophagy mediates the bulk degradation of cytoplasmic components in lysosomes/vacuoles. Five autophagy-related (Atg) proteins are involved in a ubiquitin-like protein conjugation system. Atg12 is conjugated to its sole target, Atg5, by two enzymes, Atg7 and Atg10. The Atg12–Atg5 conjugates form a multimeric complex with Atg16. Formation of the Atg12–Atg5–Atg16 ternary complex is crucial for the functions of these proteins on autophagy. Here, the expression, purification and crystallization of the Atg12–Atg5 conjugate bound to the N-terminal region of Atg16 (Atg16N) are reported. The Atg12–Atg5 conjugates were formed by co-expressing Atg5, Atg7, Atg10 and Atg12 in Eschericia coli. The Atg12–Atg5–Atg16N ternary complex was formed by mixing purified Atg12–Atg5 conjugates and Atg16N, and was further purified by gel-filtration chromatography. Crystallization screening was performed by the free-interface diffusion method. Using obtained microcrystals as seeds, large crystals for diffraction data collection were obtained by the sitting-drop vapour-diffusion method. The crystal contained one ternary complex per asymmetric unit, and diffracted to 2.6 Å resolution.

Trimeric structure and conformational equilibrium of M-ficolin fibrinogen-like domain

Tanio, M. — 2008-05-01

Ficolins are pathogen-recognition molecules in innate immune systems. The crystal structure of the human M-ficolin recognition domain (FD1) has been determined at 1.9 Å resolution, and compared with that of the human fibrinogen γ fragment, tachylectin-5A, L-ficolin and H-ficolin. The overall structure of FD1 is similar to that of the other proteins, although the peptide bond between Asp282 and Cys283, which is in a predicted ligand-binding site, is a normal trans bond, unlike the cases of the other proteins. Analysis of the pH-dependent ligand-binding activity of FD1 in solution suggested that a conformational equilibrium between active and non-active forms in the ligand-binding region, involving cis-trans isomerization of the Asp282—Cys283 peptide bond, contributes to the discrimination between self and non-self, and that the pKa values of His284 are 6.1 and 6.3 in the active and non-active forms, respectively.

Engines of Discovery (A Century of Particle Accelerators). By Andrew Sessler and Edmund Wilson. Pp. ix + 212. Hackensack, NJ: World Scientific Publishing 2007. Price: (hardcover) GBP 29, USD 54. ISBN 978-981-270-070-4.

Suller, V.P. — 2008-01-01

Structural insights into the similar modes of Nrf2 transcription factor recognition by the cytoplasmic repressor Keap1

Padmanabhan, B. — 2008-05-01

The cytoplasmic repressor Keap1 regulates the function of transcription factor Nrf2 which plays critical roles in oxidative and xenobiotic stresses. The Neh2 domain of Nrf2 interacts with Keap1 at the bottom region of the Kelch/β-propeller domain which is formed by double-glycine repeat and C-terminal region domains (Keap1-DC). The structure of Keap1-DC complexed with an Nrf2 peptide containing a conserved DLG motif has been determined at 1.9 Å resolution. The Keap1-bound DLG peptide possesses a hairpin conformation, and it binds to the Keap1 protein at the bottom region of the β-propeller domain. The intermolecular interaction occurs through their complementary electrostatic interactions. Comparison of the present structure with the recently reported Keap1-DC complex structure suggests that the DLG and ETGE motifs of Neh2 in Nrf2 bind to Keap1 in a similar manner but with different binding potencies.

Current events

2007-11-01

Current events

2007-09-01

Coherent X-ray scattering and lensless imaging at the European XFEL Facility

Vartanyants, I.A. — 2007-11-01

Coherent X-ray diffraction imaging is a rapidly advancing form of lensless microscopy. The phase information of the diffraction pattern is embedded in a sufficiently sampled coherent diffraction pattern. Using advanced computational methods, this diffraction pattern can be inverted to produce an image of a sample with diffraction-limited resolution. It is attractive to use high-power coherent X-ray beams produced by future X-ray free-electron lasers for imaging nanoscale condensed matter, materials and biological samples. Here, the scientific case, requirements and the possible realisation of the coherent X-ray diffraction imaging beamlines at the European XFEL Facility are presented.

Current events

2007-07-01

Developing 100 ps-resolved X-ray structural analysis capabilities on beamline NW14A at the Photon Factory Advanced Ring

Nozawa, S. — 2007-07-01

NW14A is a newly constructed undulator beamline for 100 ps time-resolved X-ray experiments at the Photon Factory Advanced Ring. This beamline was designed to conduct a wide variety of time-resolved X-ray measurements, such as time-resolved diffraction, scattering and X-ray absorption fine structure. Its versatility is allowed by various instruments, including two undulators, three diffractometers, two pulse laser systems and an X-ray chopper. The potential for the detection of structural changes on the 100 ps time scale at NW14A is demonstrated by two examples of photo-induced structural changes in an organic crystal and photodissociation in solution.

ID20: a beamline for magnetic and resonant X-ray scattering investigations under extreme conditions

Paolasini, L. — 2007-07-01

A new experimental station at ESRF beamline ID20 is presented which allows magnetic and resonant X-ray scattering experiments in the energy range 3–25 keV to be performed under extreme conditions. High magnetic field up to 10 T, high pressure up to 30 kbar combined with low temperatures down to 1.5 K are available and experiments can be performed at the M-edges of actinide elements, L-edges of lanthanides and K-edges of transition metals.

The small-angle and wide-angle X-ray scattering set-up at beamline BL9 of DELTA. Erratum

Krywka, C. — 2007-07-01

A correction is made to the equation in Krywka et al. (2007), J. Synchrotron Rad. 14, 244–251.

Current events

2007-05-01

Current events

2007-03-01

Progress in research into radiation damage in cryo-cooled macromolecular crystals

Garman, E.F. — 2007-01-01

Current events

2007-01-01

Verifying DiffEXAFS measurements with differential X-ray diffraction

Ruffoni, M.P. — 2007-01-01

Differential EXAFS (DiffEXAFS) is a novel technique for measuring atomic perturbations on a local scale. Here a complementary technique for such studies is presented: differential X-ray diffraction (DiffXRD), which may be used to independently verify DiffEXAFS results whilst using exactly the same experimental apparatus and measurement technique. A test experiment has been conducted to show that DiffXRD can be used to successfully determine the thermal expansion coefficient of SrF2.

Dose dependence of radiation damage for protein crystals studied at various X-ray energies

Shimizu, N. — 2007-01-01

Radiation damage to protein crystals is the most serious problem in obtaining accurate structures from protein crystallography. In order to examine the photon energy dependence of radiation damage, 12 to 15 data sets from each of nine tetragonal lysozyme crystals were collected at nine different X-ray energies (6.5, 7.1, 8.3, 9.9, 12.4, 16.5, 20.0, 24.8 and 33.0 keV) using beamline BL41XU at SPring-8. All results were compared on the basis of absorbed dose, expressed in Gray (Gy). Crystallographic statistics, such as the values of lattice constants, Rmerge and I/σ(I), for each data set degraded at all nine energies as the exposure time for each crystal increased. In all data sets, radiation damage was observed after the absorbed dose exceeded 106 Gy. However, from the point of view of crystallographic statistics normalized to the absorbed dose, no clear dependence on photon energy was observed in these results. Structural refinement showed that the average B-factor for the last data set was larger than that for the first data set at all energies tested. However, no energy dependence of radiation damage on B-factor was found. Furthermore, disruption of disulfide bonds due to radiation damage was observed in electron density maps even at the highest photon energy (33 keV) used in this study. Therefore, these results suggest that radiation damage in the energy range investigated could be evaluated based on absorbed dose without energy dependence, and that it is important to minimize the absorbed dose in a crystal sample for obtaining an accurate protein structure.

XANES measurements of the rate of radiation damage to selenomethionine side chains

Holton, J.M. — 2007-01-01

The radiation-induced disordering of selenomethionine (SeMet) side chains represents a significant impediment to protein structure solution. Not only does the increased B-factor of these sites result in a serious drop in phasing power, but some sites decay much faster than others in the same unit cell. These radio-labile SeMet side chains decay faster than high-order diffraction spots with dose, making it difficult to detect this kind of damage by inspection of the diffraction pattern. The selenium X-ray absorbance near-edge spectrum (XANES) from samples containing SeMet was found to change significantly after application of X-ray doses of 10–100 MGy. Most notably, the sharp `white line' feature near the canonical Se edge disappears. The change was attributed to breakage of the Cγ—Se bond in SeMet. This spectral change was used as a probe to measure the decay rate of SeMet with X-ray dose in cryo-cooled samples. Two protein crystal types and 15 solutions containing free SeMet amino acid were examined. The damage rate was influenced by the chemical and physical condition of the sample, and the half-decaying dose for the selenium XANES signal ranged from 5 to 43 MGy. These decay rates were 34- to 3.8-fold higher than the rate at which the Se atoms interacted directly with X-ray photons, so the damage mechanism must be a secondary effect. Samples that cooled to a more crystalline state generally decayed faster than samples that cooled to an amorphous solid. The single exception was a protein crystal where a nanocrystalline cryoprotectant had a protective effect. Lowering the pH, especially with ascorbic or nitric acids, had a protective effect, and SeMet lifetime increased monotonically with decreasing sample temperature (down to 93 K). The SeMet lifetime in one protein crystal was the same as that of the free amino acid, and the longest SeMet lifetime measured was found in the other protein crystal type. This protection was found to arise from the folded structure of the protein molecule. A mechanism to explain observed decay rates involving the damaging species following the electric field lines around protein molecules is proposed.

Radioprotectant screening for cryocrystallography

Southworth-Davies, R.J. — 2007-01-01

Radiation damage continues to present a problem to crystallographers using cryocooled protein crystals at third-generation synchrotrons. Free-radical scavengers have been suggested as a possible means of reducing the rate of this damage. The screening of a large number of potential radioprotectants was undertaken with an online microspectrophotometer using cystine and cysteine to model protein disulfide bonds and thiol groups, respectively. Oxidized α-lipoic acid was tested as a possible model disulfide bond. The evidence for the effectiveness of ascorbate as a radioprotectant was strengthened, and quinone, 2,2,6,6-tetramethyl-4-piperidone, and reduced dithiothreitol showed promise as radioprotectants.

X-ray radiation-induced damage in DNA monitored by online Raman

McGeehan, J.E. — 2007-01-01

High-quality Raman spectra have been collected on single DNA crystals kept at 100 K in a flow of cold nitrogen gas prior, during and after macromolecular crystallography (MX) data collection. The non-symmetric bending vibration for C—Br bonds in 8-bromo-2′-deoxyguanosine has been unambiguously identified at 293 cm−1 in the non-resonant Raman spectra. The breakage of this bond could be monitored by the continuous recording of Raman spectra during X-ray exposure, and its decay versus dose could be directly correlated with the loss of the bromide definition within the electron-density maps as determined with MX.

Plastic-embedded protein crystals

Ravelli, R.B.G. — 2007-01-01

Rapid vitrification followed by the replacement of the vitrified water by a solvent (freeze substitution) and then resin is a widely used procedure for preparing biological samples for electron microscopy. The resulting plastic-embedded samples permit convenient room-temperature sectioning (microtomy) and can yield well preserved cellular structures. Here this procedure has been applied to crystalline protein samples, and it is shown that it is possible to freeze-substitute vitrified crystals while preserving some of their original diffraction properties. The plastic-embedded crystals were used to collect a series of complete room-temperature data sets at a powerful macromolecular crystallography synchrotron beamline. Whereas one normally observes specific damage to disulfide bonds upon X-ray radiation, no such damage was seen for the plastic-embedded sample. The X-ray diffraction data allowed an initial atomic analysis to be made of the effects of freeze-substitution and plastic embedding on biological samples.

Current events

2006-11-01

Calibration of spectra from dispersive XAS beamlines

Ruffoni, M.P. — 2006-11-01

The DXAS Calibration computer program provides a quantitative and automated solution to the problem of calibrating spectra from dispersive XAS beamlines. Such spectra, obtained in arbitrary energy units, are calibrated with respect to the absorption features of a supplied reference spectrum, which has been obtained under similar conditions on a calibrated beamline. In addition to basic energy coordinate transformation parameters, DXAS Calibration supplies instrument corrections to compensate for mismatches in instrument response functions between the dispersive and reference beamlines.

Current events

2006-09-01

Stable top-up operation at SPring-8

Tanaka, H. — 2006-09-01

Top-up operation allows SPring-8 to provide highly stable X-ray beams with arbitrary filling patterns. The implementation of top-up operation is described, with a focus on the simultaneous achievement of stability of stored current, beam orbit, purity of an isolated single bunch, and beam injection efficiency. Stored-current fluctuations have been routinely reduced to a level of 10−3. Stored-beam oscillation on frequent beam injection, which was originally regarded as the most serious problem, has been successfully suppressed to a sufficiently low level that it never perturbs imaging experiments. Current impurities in nominally empty buckets have been reduced to a level of 10−9 over more than one week of operation, making possible the measurement of time-resolved spectra using high-current bunches. Finally, excellent injection efficiency, higher than 80%, is routinely obtained, even for small undulator gaps, which is critical for preventing radiation damage to insertion-device magnets and to reduce leakage radiation. The process of achieving highly stabilized top-up operation at SPring-8 and its utility for user experiments are described.

Current events

2006-07-01

Sharp-focusing Bragg–Fresnel zone plate with Laue diffraction geometry

Haroutunyan, L. — 2006-07-01

The impact of decreased zone height on the focal properties of hard X-ray Bragg–Fresnel zone plates has been studied by numerical simulation. Decreased zone height allows for smaller zone widths and, although the efficiency of the lens is decreased, the signal-to-background ratio in the focal plane of the lens remains at a comparatively high level. This is distinct from an analogous case of ordinary phase zone plates.

Reciprocal space mapping and single-crystal scattering rods. Erratum

Smilgies, D.-M. — 2006-07-01

While assembling the high-resolution graphics for Fig. 2 of Smilgies et al. [J. Synchrotron Rad. (2005). 12, 807–811], the curve from the bottom panel was erroneously repeated in the top panel. Below is the corrected figure.

Current events

2006-05-01

Multiple-pass monochromators

Schoeffel, E. — 2006-05-01

Evaluation of imaging performance of a taper optics CCD `FReLoN' camera designed for medical imaging

Coan, P. — 2006-05-01

The purpose of this work was to assess the imaging performance of an indirect conversion detector (taper optics CCD `FReLoN' camera) in terms of the modulation transfer function (MTF), normalized noise power spectrum (NNPS) and detective quantum efficiency (DQE). Measurements were made with a synchrotron radiation laminar beam at various monochromatic energies in the 20–51.5 keV range for a gadolinium-based fluorescent screen varying in thickness; data acquisition and analysis were made by adapting to this beam geometry protocols used for conventional cone beams. The presampled MTFs of the systems were measured using an edge method. The NNPS of the systems were determined for a range of exposure levels by two-dimensional Fourier analysis of uniformly exposed radiographs. The DQEs were assessed from the measured MTF, NNPS, exposure and incoming number of photons. The MTF, for a given screen, was found to be almost energy independent and, for a given energy, higher for the thinnest screen. At 33 keV and for the 40 (100) µm screen, at 10% the MTF is 9.2 (8.6) line-pairs mm−1. The NNPS was found to be different in the two analyzed directions in relation to frequency. Highest DQE values were found for the combination 100 µm and 25 keV (0.5); it was still equal to 0.4 at 51.5 keV (above the gadolinium K-edge). The DQE is limited by the phosphor screen conversion yield and by the CCD efficiency. At the end of the manuscript the results of the FReLoN characterization and those from a selected number of detectors presented in the literature are compared.

Comments on A new model for statistical error analysis in XAS: about the distribution function of the absorption coefficient by E. Curis & S. Bénazeth (2001). J. Synchrotron Rad. 8, 264–266

Nadarajah, S. — 2006-05-01

Response to S. Nadarajah & S. Kotz's Comments on A new model for statistical error analysis in XAS: about the distribution function of the absorption coefficient by E. Curis & S. Bénazeth (2001). J. Synchrotron Rad. 8, 264–266

Curis, E. — 2006-05-01

Structure Determination by X-ray Crystallography. By Mark Ladd and Rex Palmer. Pp. xlii + 819. New York: Kluwer Academic/Plenum, 4th ed., 2003. Price (paperback) GBP 41, ISBN 0-306-47454-9.

Ohashi, Y. — 2006-05-01

Current events

2006-03-01

Introduction to the Special Issue on Detectors

Graafsma, H. — 2006-03-01

Current events

2006-01-01

Current events

2005-11-01

Deep UV and vacuum ultraviolet spectrophotometer

Schoeffel, E. — 2005-11-01

A transparent two-dimensional in situ beam-position and profile monitor for synchrotron X-ray beamlines

Kyele, N.R. — 2005-11-01

A compact, inexpensive and easy-to-construct two-dimensional in situ beam-position and profile monitor for synchrotron X-ray beamlines is presented. The device is based on the collection of spatially resolved scattered radiation from a polyimide foil. The X-ray beam passes through a foil placed in the path of the beam, which absorbs no more than 3% of the beam at 12 keV. The scattered radiation is collected at an angle of 90° through a collimator located below the foil onto a CCD sensor. The device was tested on bending-magnet beamline BM26 at the ESRF synchrotron radiation source and has a positional sensitivity better than 10 µm with a large working range of 25 mm × 25 mm. Although the device is optimized for use in the range 10–12 keV, it can easily be modified for use with higher-energy beams by using a suitably chosen scattering foil.

Synchrotron radiation and nanobiosciences – introductory overview

Pechkova, E. — 2005-11-01

Some introductory remarks on microbeam diffraction in nanobiosciences

Paris, O. — 2005-11-01

Current events

2005-09-01

1 m vacuum monochromator

Schoeffel, E. — 2005-09-01

Structure determination by single-crystal X-ray diffraction (SXD) at megabar pressures

Dera, P. — 2005-09-01

Structures from powders and poor-quality single crystals at high pressure

McMahon, M.I. — 2005-09-01

The use of single-crystal techniques and quasi-single-crystal samples in solving and refining complex crystal structures at high pressure is reviewed. In particular, recent studies of the incommensurate and modulated structures found in a number of elemental metals at high pressure are focused on.

Advances in array detectors for X-ray diffraction techniques

Hanley, Q.S. — 2005-09-01

Improved focal plane array detector systems are described which can provide improved readout speeds, random addressing and even be employed to simultaneously measure position, intensity and energy. This latter capability promises to rekindle interests in Laue techniques. Simulations of three varieties of foil mask spectrometer in both on- and off-axis configurations indicate that systems of stacked silicon detectors can provide energy measurements within 1% of the true value based on the use of single `foils' and ∼10000 photons. An eight-detector hybrid design can provide energy coverage from 4 to 60 keV. Energy resolution can be improved by increased integration time or higher flux experiments. An off-axis spectrometer design in which the angle between the incident beam and the detector system is 45° results in a shift in the optimum energy response of the spectrometer system. In the case of a 200 µm-thick silicon absorber, the energy optimum shifts from 8.7 keV to 10.3 keV as the angle of incidence goes from 0 to 45°. These new designs make better use of incident photons, lower the impact of source flicker through simultaneous rather than sequential collection of intensities, and improve the energy range relative to previously reported systems.

High-pressure polymorphism of cyclopentanol (C5H10O): the structure of cyclopentanol phase-V at 1.5 GPa

Moggach, S.A. — 2005-09-01

The fully ordered high-pressure crystal structure of cyclopentanol (C5H10O) has been solved using single-crystal X-ray diffraction techniques on station 9.8 at the SRS Daresbury Laboratory. At pressures above 1.5 GPa, cyclopentanol crystallizes in the monoclinic P21/c space group with a = 17.882 (3), b = 5.4573 (3), c = 9.6817 (14) Å, β = 104.699 (8)° and Z′ = 2. The crystal structure is characterized by the formation of hydrogen-bonded molecular chains, denoted C_2^2(4) in graph set notation, which lie parallel to the crystallographic c-axis, with the molecules adopting a pseudo fourfold arrangement around the central core of hydrogen bonds.

The effect of pressure on the crystal structure of hexagonal l-cystine

Moggach, S.A. — 2005-09-01

The crystal structure of hexagonal l-cystine has been determined at room temperature at pressures between 0.4 and 3.7 GPa; unit-cell dimensions were measured up to 6.4 GPa. The structure of this phase consists of molecules in their zwitterionic form, and crystallizes in the hexagonal space group P6122. The structure consists of hydrogen-bonded layers which are strongly reminiscent of those seen in α-glycine, and consist of R_4^4(16) hydrogen-bonded ring motifs. These layers are connected on one side by the disulfide bridges within the cystine molecules, and on the other by NH⋯O hydrogen bonds to other glycine-like layers. The most compressible unit-cell dimension, and the direction of greatest strain in the structure, is along the c-axis, and application of pressure pushes the layers closer together. The compression occurs approximately equally in the regions of the interlayer hydrogen bonds and the disulfide bridges; in the latter, changes in the C—S—S—C torsion angles allow the cystine molecules to act like springs. The effects of pressure can be interpreted in terms of closing-up of voids in the structure, and this leads to (i) a lessening of the N—C—C—O and C—S—S—C torsional angles, (ii) shortening of the N—H⋯O hydrogen bonds by 0.10–0.60 Å and (iii) a further shortening of an already short S⋯S contact from 3.444 (4) Å to 3.264 (4) Å.

Current events

2005-07-01

Variable-period undulators as synchrotron radiation sources. Erratum

Shenoy, G.K. — 2005-07-01

Citations are added to the paper by Shenoy et al. [J. Synchrotron Rad. (2003). 10, 205–213].

Application notes on the use of softer X-rays for anomalous powder diffraction

Cernik, R.J. — 2005-07-01

An in-vacuum diffractometer has been modified to collect powder diffraction data from a sample of promazine hydrochloride. Strong anomalous contrast has been observed at, or close to, the sulphur edge. Based on the data collected, a bespoke diffractometer has been designed that, together with minor changes to the geometry of the experiment, will enable the routine collection of powder data at absorption edges below 5.5 keV.

The uses of softer X-rays in structural studies

Cernik, R.J. — 2005-07-01

Nanoarchitectures of the animal extracellular matrix: opportunities for synchrotron radiation studies on collagen and fibrillin

Wess, T.J. — 2005-11-01

The extracellular matrix comprises structures that support the architectural organization of virtually all animal tissues. Within this architecture, two classes of protein assemblies found as long slender fibrils (collagen and fibrillin) characterize the bulk of the extracellular matrix. In both classes of fibrous protein, the molecular organization within a fibril ensures that the properties of the individual molecules transcend to the nanostructural and mesoscopic levels of structural organization and thence the tissue itself. The composition of the fibrils, in conjunction with other biomolecules and their suprafibrillar architecture, facilitates the formation of tissues as diverse as skin, tendon, cornea ciliary zonules and aorta. Here the relative tear resistance, strength, transparency and optical properties are paramount for proper function. Many structural investigations of fibrous protein structure have relied heavily on the use of synchrotron radiation in order to elucidate molecular packing, primarily due to the distinct benefits that X-ray diffraction provides, such as minimal sample preparation, rapid data collection and in situ mechanical testing. In this paper, an overview of the investigations that have revealed different levels of molecular architecture in fibril-based tissues is presented. Emerging future technology and how this can be matched with the pressing questions in extracellular matrix biology are also discussed.

Current events

2005-05-01

A high-throughput structural biology/proteomics beamline at the SRS on a new multipole wiggler

Cianci, M. — 2005-07-01

The North West Structural Genomics Centre's beamline, MAD10, at the SRS receives the central part of the radiation fan (0.5 mrad vertically, 4 mrad horizontally) produced by a new 2.46 T ten-pole wiggler. The optical arrangement of the beamline consists of a Rh-coated collimating Si mirror, a fixed-exit-beam double-crystal monochromator with sagittal bending for horizontal focusing and a second Rh-coated Si mirror for vertical focusing. The double-crystal Si (111) monochromator allows data collection in the 5–13.5 keV photon energy range with rapid (subsecond) tunability and high energy resolution. The monochromatic beam is optimized through a 200 µm collimator. The beamline end station has been designed around a Mar desktop beamline with high-throughput cryogenic sample changer, Mar225 CCD detector, liquid-N2 autofill system and an ORTEC C-TRAIN-04 energy-resolving high-count-rate X-ray fluorescence detector. The instrument is optimized for MAD/SAD applications in protein crystallography with the additional mode of operation of online single-crystal EXAFS studies on the same crystals. Thus, screening of metals/Se in the crystal can be performed quickly prior to MAD/SAD data collection by exciting the crystal with X-rays of appropriate energy and recording an energy-dispersive fluorescence spectrum. In addition, this experimental set-up allows for parallel XAFS measurements on the same crystal to monitor `radiation-induced' changes, if any, in e.g. the redox state of metal centres to be detected for a `metallic' functional group during crystallographic data collection. Moreover, careful minimization of the thickness of the Be window maximizes the intensity performance for the 2.0–2.5 Å softer wavelength range. This range also covers the K-edges of a number of important 3d transition metals as well as the L-edges of xenon and iodine and enhanced sulfur f ′′.

Resonant soft X-ray diffraction – in extremis

Hatton, P.D. — 2005-07-01

The use of softer-energy X-rays produced by synchrotron radiation for diffraction is an area of current interest. In this paper, experiments exploiting resonant scattering at the L absorption edges of 3d transition metal elements are reported. Such energies, typically 500–1000 eV, are at the extreme limit of soft X-ray diffraction where absorption effects are so severe that the sample and diffractometer must be placed in a windowless high-vacuum vessel. In addition, the Ewald sphere is so small as to likely contain, at most, only a single Bragg reflection. Advantages of using such radiation for the study of weak diffraction effects such as anomalous scattering, charge ordering, magnetic diffraction and orbital ordering are reported.

Overcoming protein denaturation caused by irradiation in a high-flux synchrotron radiation circular dichroism beamline

Janes, R.W. — 2005-07-01

It has been established that the new circular dichroism beamline CD12 has sufficiently high flux at low wavelengths to cause apparent irradiation problems with protein samples while their synchrotron radiation circular dichroism (SRCD) spectra are being collected. The cause of this effect has been extensively investigated and is reported in an accompanying paper [Wien et al. (2005). J. Synchrotron Rad. 12, 517–523.]. Experiments suggest that localized heating of the protein sample, leading to denaturation, is the probable cause. Methods to circumvent this problem by limiting the beam flux are reported. This was achieved using either an attenuation cell of water placed beam-side of the sample cell, or limiting the beam cross-sectional area hitting the sample. Such methods are shown to result in substantial reduction or apparent complete removal of this protein denaturation over the course of collecting three successive spectra. Elimination of this denaturation problem enables multiple SRCD scans for protein samples to be collected, which are vital both for good practice and for statistically valid results.

Towards an understanding of radiation damage in cryocooled macromolecular crystals

Nave, C. — 2005-05-01

Interest in radiation damage is growing rapidly owing to the surge in macromolecular crystallography experiments carried out at modern brilliant synchrotron macromolecular crystallography beamlines. Work on the characterization of radiation damage in cryocooled protein crystals is starting to have some impact on our understanding of the problem and of how damage might be affecting both the process of structure solution and the actual structure obtained. A brief review of the most recent developments is given together with an assessment of the remaining problems. Although progress is being made, the understanding of radiation damage is far from complete. Methods for recognizing the damage and treating the data are being made available but they are still at an early stage of development.

VUV irradiation effects on proteins in high-flux synchrotron radiation circular dichroism spectroscopy

Wien, F. — 2005-07-01

Synchrotron radiation circular dichroism (SRCD) spectroscopy is emerging as an important new tool in structural molecular biology. Previously we had shown that in lower-flux SRCD instruments, such as UV1 at ISA and beamline 3.1 at the SRS, vacuum ultraviolet (VUV) radiation damage to proteins was not evident after exposure over a period of hours. No effects were detected in either the protein primary or the secondary structures. However, with the development of high-flux beamlines, such as CD12 at the SRS, this issue has been revisited because of changes observed in the SRCD spectra of consecutive scans of protein samples obtained on this high-flux beamline. Experiments have been designed to distinguish between two different possible mechanisms: (i) photoionization causing free radicals or secondary electrons producing degradation of the protein, and (ii) local heating of the sample resulting in protein denaturation. The latter appears to be the principal source of the signal deterioration.

Brightness, spectral brightness or brilliance – Report of the Working Group on Synchrotron Radiation Nomenclature

Mills, D.M. — 2005-05-01

Current events

2005-03-01

Applications of synchrotron radiation to materials research

Shenoy, G. — 2005-03-01

Microfocus X-ray scattering investigations of eggshell nanotexture

Lammie, D. — 2005-11-01

The avian eggshell is a highly ordered calcitic bioceramic composite, with both inorganic and organic constituents. The interactions between the inorganic and organic components within the structure are poorly understood but are likely to occur at the nanometre level. Thus structural variation at this level may impinge on the overall structural integrity and mechanical performance of the eggshell, and therefore analysis at this level is fundamental in fully understanding this ordered structure. In this study, structural changes in the mineral crystallites were investigated by microfocus small-angle X-ray scattering (µSAXS) using synchrotron radiation. Small-angle X-ray scattering (SAXS) can be used to investigate structures on the nanometre scale such as size, shape, arrangement and internal porosity. A microfocused X-ray beam, 1.5 µm vertically by 7 µm, was used to produce vertical linear scans of the eggshell section. SAXS patterns were taken from the eggshell membrane (inner surface of the eggshell) to the cuticle (outer surface of the eggshell). This allowed textural variations within the eggshell to be mapped. The scattering intensity profile was then used to derive the dimension of scattering objects that define the nanotexture. The nanotexture observed may result from the presence of the organic matrix, which is embedded as intracrystalline particles producing voids within the calcified framework of large (>1 µm) calcite crystals. Porod analysis revealed the average size of a scattering interface to be approximately 4.5 nm with small changes that had a depth-dependent variation. These were largest at the mammillary layer/membrane boundary. The palisade layer displayed a small upward trend in size of scattering object. Parallel scans showed that the textural variations observed within the palisade layer are significant and indicate local subtextures. In addition, many of the patterns exhibit diffuse scattering streaks that could result from reflectivity from the larger crystallite interfaces. Changes in the orientation of diffuse streaks were observed within the different layers, the membranes, mammillary layer, palisade layer, vertical crystal layer and cuticle, indicating certain preferred orientations of the crystallites within the layers. The nanotextural variations that are apparent could have implications at the macroscopic level of the resulting eggshell.

Phasing in the presence of radiation damage

Ravelli, R.B.G. — 2005-05-01

In the accurate estimation of small signals, redundancy of observations is often seen as an essential tool for the experimenter. This is particularly true during macromolecular structure determination by single-wavelength anomalous dispersion (SAD), where the exploitable signal can be less than a few percent. At the most intense undulator synchrotron beamlines, the effect of radiation damage can be such that all usable signal is obscured. Here the magnitude of this effect in experiments performed at the Se K-edge is quantified. Six successive data sets were collected on the same crystal, interspersed with two exposures to the X-ray beam during which data were not collected. It is shown that the very first data set has excellent phasing statistics, whereas these statistics degrade for the later data sets. Merging several data sets into one, highly redundant, data set only gave moderate improvements as a result of the presence of radiation damage. Part of the damage could be corrected for using a linear interpolation scheme. Interpolation of the data to a low-dose as well as to a high-dose data set allowed us to combine the SAD method with the radiation-damage induced phasing (RIP) technique, which further improved the experimental phases, especially after density modification. Some recommendations are given on how to mitigate the effect of radiation damage during structure determination.

Beam-size effects in radiation damage in insulin and thaumatin crystals

Schulze-Briese, C. — 2005-05-01

Cryocooled insulin and thaumatin crystals were irradiated in a series of alternating data collections and high-dose-rate exposures using either a vertically focused or vertically defocused beam. The main result is that the radiation damage is limited to the exposed region, which can be explained by the short range of the photoelectrons and the Auger electron cascade produced by light elements. Consequently, the unexposed angular range provides significantly improved data quality and electron density compared with previously exposed angular wedges of the crystal when a vertically focused beam is used, while no differences are observed between a fresh wedge and an exposed region for the vertically defocused beam. On the other hand, the focused beam provides higher I/σI ratios at high resolution than homogeneous sample illumination but also causes more rapid sample deterioration.

Parameters affecting the X-ray dose absorbed by macromolecular crystals

Murray, J.W. — 2005-05-01

The lifetime of a macromolecular crystal in an X-ray beam is assumed to be limited by the absorbed dose. This dose, expressed in Gray (Gy = J kg−1), is a function of a number of parameters: the absorption coefficients of the constituent atoms of the crystal, the number of molecules per asymmetric unit, the beam energy, flux, size and profile, the crystal size, and the total irradiation time. The effects of these variables on the predicted absorbed dose, calculated using the program RADDOSE, are discussed and are illustrated with reference to the irradiation of a selenomethionine protein crystal of unknown structure. The results of RADDOSE can and will in the future be used to inform the data collection procedure as it sets a theoretical upper limit on the total exposure time at a certain X-ray source. However, as illustrated with an example for which the experimental data are compared with prediction, the actual lifetime of a crystal could become shorter in those cases where specific damage breaks down crucial crystal contacts.

Current events

2005-01-01

Metallogenomics and biological X-ray absorption spectroscopy

Ascone, I. — 2005-01-01

An overview of the second special issue of the journal on biological applications of X-ray absorption spectroscopy (BioXAS) is presented. The emphasis is on the study of metalloproteins in the context of structural genomics programmes (metallogenomics).

The use of softer X-rays in the structure elucidation of microporous materials

Helliwell, M. — 2005-07-01

Microporous materials, such as zeolites and aluminophosphates, have many applications as molecular sieves and shape-selective catalysts. This is due to their three-dimensional frameworks, which contain regular pores and channels, to their high acidity, arising from Brønsted and Lewis acid active sites, and to the incorporation of transition metal atoms into framework sites. This review firstly provides an introduction into the nature and properties of these materials, and their important applications; the difficulties in their full characterization and possible methods of elucidating their structures are then outlined; finally, methods of characterization, utilizing `softer X-rays' are introduced. The first method is the determination of low concentrations of transition metals, incorporated into the frameworks using single crystal anomalous dispersion crystallography; synchrotron radiation is used to tune to the absorption edge of the metal atom in question, in order to change its signal relative to that of the rest of the structure, thereby allowing the pinpointing of its positions and the determination of its concentration at each site in the framework. Secondly, the use of longer wavelengths in powder diffraction studies is described, which, by stretching out the powder pattern, thereby reduces the overlapping of the diffraction peaks, thus allowing the structure to be solved by conventional direct methods. Finally, the use of X-ray absorption spectroscopy to determine the metal incorporation and the nature of coordination at the metal atom sites, in Mn silicalite-1 and FAPO-36, are described.

An internet-based synchrotron experiment for students measuring the X-ray magnetic circular dichroism of a PtFe alloy

Paulus, M. — 2005-03-01

A new internet-based synchrotron experiment for students is presented. A polarimeter and computer software have been developed for measuring via the internet the X-ray magnetic circular dichroism of PtFe around its Pt LII and LIII absorption edges. From the experiment, students can examine the X-ray magnetic circular dichroism of a thin PtFe foil utilizing circular-polarized synchrotron radiation emitted by the superconducting asymmetric wiggler at the synchrotron radiation source DELTA of the University of Dortmund.

Specimen charging in X-ray absorption spectroscopy: correction of total electron yield data from stabilized zirconia in the energy range 250–915 eV

Vlachos, D. — 2005-03-01

The effects of specimen charging on X-ray absorption spectroscopy using total electron yield have been investigated using powder samples of zirconia stabilized by a range of oxides. The stabilized zirconia powder was mixed with graphite to minimize the charging but significant modifications of the intensities of features in the X-ray absorption near-edge fine structure (XANES) still occurred. The time dependence of the charging was measured experimentally using a time scan, and an algorithm was developed to use this measured time dependence to correct the effects of the charging. The algorithm assumes that the system approaches the equilibrium state by an exponential decay. The corrected XANES show improved agreement with the electron energy-loss near-edge fine structure obtained from the same samples.

Heterologous metalloprotein biosynthesis in Escherichia coli: conditions for the overproduction of functional copper-containing nitrite reductase and azurin from Alcaligenes xylosoxidans

Harris, R.L. — 2005-01-01

This paper reports on the optimization of conditions for the overproduction and isolation of two recombinant copper metalloproteins, originally encoded on the chromosome of the dentrifying soil bacterium Alcaligenes xylosoxidans, in the heterologous host Escherichia coli. The trimeric enzyme nitrite reductase (NiR) contains both type-1 and type-2 Cu centres, whilst its putative redox partner, azurin I, is monomeric and has only a type-1 Cu centre. Both proteins were processed and exported to the periplasm of E. coli, which is consistent with their periplasmic location in their native host A. xylosoxidans. NiR could be readily purified from the periplasmic fraction of E. coli but the enzyme as isolated possessed only type-1 Cu centres. The type-2 Cu centre could be fully reconstituted by incubation of the periplasmic fraction with copper sulfate prior to enzyme purification. Azurin I could only be isolated with a fully occupied type-1 centre when isolated from the crude cell extract but not after isolation from the periplasmic fraction, suggesting loss of the copper due to proteolysis. Based on a number of criteria, including spectroscopic, mass spectrometric, biochemical and structural analyses, both recombinant proteins were found to be indistinguishable from their native counterparts isolated from A. xylosoxidans. The findings of this work have important implications for the overproduction of recombinant metalloproteins in heterologous hosts.

Towards the high-throughput expression of metalloproteins from the Mycobacterium tuberculosis genome

Hall, J.F. — 2005-01-01

The provision of high-quality protein in adequate quantities is a prerequisite for any structural genomics programme. A number of proteins from the Mycobacterium tuberculosis genome have been expressed and the success at each stage of the process assessed. Major difficulties have been encountered in the purification and solubilization of many of these proteins, most likely as a result of mis-folding. Some improvements have been made to the protocol but the overall success rate is still limited; however, the use of a cell-free protein expression system will circumvent some of the difficulties encountered. Alternative purification systems are also required and the properties of a mutant blue copper protein are described, that may offer a combined purification and tagging system.

Softer and soft X-rays in macromolecular crystallography

Djinović Carugo, K. — 2005-07-01

The utilization and the potential of softer and soft X-rays in macromolecular crystallography as well as the challenges associated with the corresponding diffraction experiments and their possible remedies are reviewed.

Current events

2004-11-01

Comments on Treatment of EXAFS data taken in the fluorescence mode in non-linear conditions by G. Ciatto et al. (2004). J. Synchrotron Rad. 11, 278–283

Warburton, W.K. — 2004-11-01

Response to W. K. Warburton's Comments on Treatment of EXAFS data taken in the fluorescence mode in non-linear conditions by G. Ciatto et al. (2004). J. Synchrotron Rad. 11, 278–283

Ciatto, G. — 2004-11-01

Aberration corrected vacuum ultraviolet monochromator

Schoeffel, E. — 2004-09-01

The BioCAT undulator beamline 18ID: a facility for biological non-crystalline diffraction and X-ray absorption spectroscopy at the Advanced Photon Source

Fischetti, R. — 2004-09-01

The 18ID undulator beamline of the Biophysics Collaborative Access Team at the Advanced Photon Source, Argonne, IL, USA, is a high-performance instrument designed for, and dedicated to, the study of partially ordered and disordered biological materials using the techniques of small-angle X-ray scattering, fiber diffraction, and X-ray absorption spectroscopy. The beamline and associated instrumentation are described in detail and examples of the representative experimental results are presented.

Carl-Ivar Brändén, 1934–2004

Schneider, G. — 2004-09-01

Cullie Sparks, 1929–2004

Ice, G.E. — 2004-07-01

Image quality improvement in a hard X-ray projection microscope using total reflection mirror optics

Mimura, H. — 2004-07-01

A new figure correction method has been applied in order to fabricate an elliptical mirror to realize a one-dimensionally diverging X-ray beam having high image quality. Mutual relations between figure errors and intensity uniformities of diverging X-ray beams have also been investigated using a wave-optical simulator and indicate that figure errors in relatively short spatial wavelength ranges lead to high-contrast interference fringes. By using a microstitching interferometer and elastic emission machining, figure correction of an elliptical mirror with a lateral resolution close to 0.1 mm was carried out. A one-dimensional diverging X-ray obtained using the fabricated mirror was observed at SPring-8 and evaluated to have a sufficiently flat intensity distribution.

A large-area CMOS imager as an X-ray detector for synchrotron radiation experiments

Yagi, N. — 2004-07-01

The performance of a CMOS flatpanel imager from Hamamatsu Photonics (C7942) has been tested in various synchrotron radiation experiments. This detector has a detection area of about 120 mm × 120 mm with 0.05 mm pixels, and a frame rate of 2 s−1. The commercially available product was insensitive to X-rays with an energy lower than 15 keV, but slight modifications solved this problem. Images obtained in small-angle scattering, protein crystallography and medical imaging experiments were all of high quality. The fast readout and the large area are advantageous in real-time imaging. Although its noise level is higher than the area detectors that are currently used in synchrotron radiation experiments, it is particularly useful in experiments where other bulky detectors cannot be used. Its relatively low price (about USD 30000) makes it a unique option in the choice of detectors.

Soft X-ray resonant magnetic scattering from a Ni layer with modulated magnetic anisotropy

Haznar, A. — 2004-05-01

Soft X-ray resonant magnetic scattering studies on a magnetically modulated, but nominally chemically homogenous, 5 nm Ni layer in a Cu/Ni/Cu/Co/NiO/GaAs(110) system are reported. It was possible to estimate the main chemical structure of the sample on the basis of the results from specular reflectivity and rocking scans, probing the scattering vector components in the perpendicular and in-plane direction to the Ni wires, respectively. The magnetic scattering using polarized X-rays demonstrates the magnetic modulation of the Ni layer.

XAFS imaging of Tsukuba gabbroic rocks: area analysis of chemical composition and local structure

Mizusawa, M. — 2004-03-01

Gabbroic rocks were collected at Mount Tsukuba in Japan, and their XAFS images were studied using a projection-type X-ray fluorescence (XRF) microscope, which is a powerful new tool recently developed for extremely rapid imaging. The instrument employs a grazing-incidence arrangement in order that primary X-rays illuminate the whole sample surface, as well as parallel-beam optics and an extremely close geometry in order to detect XRF by a high-performance X-ray CCD system with 1024 × 1024 pixels. The XRF image indicated that black amphibole and white feldspar, both of which are typical mineral textures of the rock, contain iron. The origin has been suggested to be several small yellowish-brown minerals contained there. The XAFS imaging has been carried out by repeating the exposure of XRF images during the energy scan of the primary X-rays. It has been found that the structure is qualitatively close to that of olivine, and the main differences found in both areas can be explained as a difference in iron and magnesium concentration, i.e. the mixed ratio of forsterite (Mg2SiO4) and fayalite (Fe2SiO4). The feasibility of the present XAFS imaging method has been demonstrated for realistic inhomogeneous minerals.

Recent developments in the PHENIX software for automated crystallographic structure determination

Adams, P.D. — 2004-01-01

A new software system called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is being developed for the automation of crystallographic structure solution. This will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model, and facilitate structure solution for both the novice and expert crystallographer. Here, the features of PHENIXare reviewed and the recent advances in infrastructure and algorithms are briefly described.

SOLVE and RESOLVE: automated structure solution, density modification and model building

Terwilliger, T. — 2004-01-01

The software SOLVE and RESOLVE can carry out all the steps in macromolecular structure solution, from scaling and heavy-atom location through phasing, density modification and model-building in the MAD, SAD and MIR cases. SOLVE uses scoring scheme to convert the decision-making in macromolecular structure solution to an optimization problem. RESOLVE carries out the identification of NCS, density modification and automated model-building. The procedure is fully automated and can function at resolutions as low as 3 Å.

Third-Generation Hard X-ray Synchrotron Radiation Sources. Edited by D. M. Mills. New York: John Wiley, 2002. Price GBP 69.95, ISBN 0-471-31433-1.

Schneider, J. — 2003-09-01

XAFS studies of nitrogenase: the MoFe and VFe proteins and the use of crystallographic coordinates in three-dimensional EXAFS data analysis. Erratum

Strange, R.W. — 2003-03-01

One of the authors was omitted in the published version of the paper by Strange et al. [J. Synchrotron Rad. (2003), 10, 71–75]. The full author list is given above. Since the acceptance of our paper, an atomic-resolution (1.16 Å) structure of MoFe-protein has emerged [Einsle et al. (2002), Science, 297, 1696–1700]. We take this opportunity to update Table 1 of the paper, demonstrating improved agreement of the three-dimensional XAFS refinement with atomic-resolution metrical information.

Multiple-electron excitation in X-ray absorption: a simple generic model. Erratum

Roy, M. — 2003-03-01

Two typographical errors have been observed in the paper by Roy et al. [J. Synchrotron Rad. (2001), 8, 1103–1108]. Equation (16) should read\eqalign{P(\hbar\omega)={}&P(\infty)\left[{{{\pi(2n-1)!}\over{2^{2n}(n-1)!(n+1)!}}}\right]^{-1}E_B^{\,n+1/2}\cr&\times\int\limits_0^{E_{\max}}{{{E^{1/2}}\over{(E_B+E)^{n+2}[1+t_{\,o}^{\,2}\,(E_B+E)^2]}}}\,\,{\rm{d}}E,}while the correct form of equation (18) is\eqalign{P(\hbar\omega)={}&P(\infty)\left[{{{\pi(2n-1)!}\over{2^{2n}(n-1)!(n+1)!}}}\right]^{-1}\cr&\times\int\limits_1^{E_p/E_B}{{{(X-1)^{1/2}}\over{X^{n+2}[1+{\textstyle{1\over4}}\left({n-1}\right)^2(E_B/E_p)X^2]}}}\,\,{\rm{d}}X.}These typographical errors do not affect our results or conclusions.

Response to P. Suortti et al.'s and K. D. Rogers et al.'s Comments on Synchrotron fibre diffraction identifies and locates foetal collagenous breast tissue associated with breast carcinoma by V. J. James (2002). J. Synchrotron Rad. 9, 71–76

James, V. — 2003-03-01

Comments on Synchrotron fibre diffraction identifies and locates foetal collagenous breast tissue associated with breast carcinoma by V. J. James (2002). J. Synchrotron Rad. 9, 71–76

Rogers, K.D. — 2003-03-01

Comments on Synchrotron fibre diffraction identifies and locates foetal collagenous breast tissue associated with breast carcinoma by V. J. James (2002). J. Synchrotron Rad. 9, 71–76

Suortti, P. — 2003-03-01