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January 2017 issue
Includes papers presented at the 9th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples
Lund, Sweden, 9–11 March 2016
Cover illustration: (Designed by Charles S. Bury.) Top left: heatmap of results from pairwise comparison of the 1D scattering curves from a SAXS experiment on glucose isomerase (GI). Blue represents frames that show statistically strong pairwise similarity, whereas sea green shows weak pairwise similarity. Region A shows a cluster of frames exhibiting transitive pairwise similarity which were taken near the beginning of the experiment at low dose. Region B shows a large cluster of frames also exhibiting transitive pairwise similarity but which were generated when the sample had received a higher dose (see Brooks-Bartlett et al., pages 63–72). Top right: A – SAXS envelope generated using frames 1 to 11 (region A in left figure), exhibiting the expected globular shape of GI (MW = 173.85 kDa). B – SAXS envelope generated using frames 63 to 73 (high dose region B in left figure). The envelope does not exhibit the expected shape and corresponds to a much smaller molecular weight (MW = 173.85 kDa). The damage phenomenon causing this is predicted to be fragmentation. Bottom: Structure of uridine, a novel scavenger for MX and SAXS experiments, and the molecular structure of lysozyme at room temperature. Uridine increases the critical dose of lysozyme by 70% in MX experiments at room temperature, and shows scavenging properties in SAXS experiments at 40 mM concentration (see Crosas et al., pages pages 53–62).
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radiation damage
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Despite significant progress made over more than 15 years of research, structural biologists are still grappling with the issue of radiation damage suffered by macromolecular crystals induced by the resultant radiation chemistry occurring during X-ray diffraction experiments. Further insights into these effects and the possible mitigation strategies for use in both diffraction and SAXS experiments are given in eight papers in this volume.
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A systematic macromolecular crystallography investigation into the observed electron density loss around the –OH group of tyrosines, as a function of dose at 100 K, is reported. It is concluded that a probable explanation is aromatic ring disordering as opposed to –OH cleavage; occurrence of the latter mechanism is a misconception perpetuated in radiation damage literature, and is unsupported by any observations in radiation chemistry.
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A statistic based on the distribution of sets of signed anomalous differences is evaluated as a possible metric for defining the point at which the inclusion of additional data from a progressively more damaged crystal into a S-SAD phasing process will reduce the probability of successful phasing.
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The best practice for dose-limiting serial synchrotron rotation crystallography was examined through anomalous signal and single-wavelength anomalous diffraction phasing of mercury-bound luciferin regenerating enzyme. Sample rotation enabled accurate data collection with fewer diffraction images than without rotation, and an increase in resolution and anomalous signal was observed up to 3.4 MGy even though specific damage occurred after an accumulated dose of 1.1 MGy.
Helical scans are compared with standard rotation methods in single-crystal X-ray diffraction experiments and, for certain cases, the helical scan methods improve the quality of the diffraction data and the electron density maps.
The protective properties of uridine against radiation damage for small-angle X-ray scattering and macromolecular crystallography experiments at room temperature are shown. The scavenging effect of uridine is similar to, or more pronounced than, the most commonly used scavengers.
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Radiation damage analysis with experimental SAXS data allows for the quantitative comparison of the efficacy of various additive radioprotectant compounds. Relevant extensions to RADDOSE-3D and the creation of a new visualization library to enable this study are presented.
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The conformational variation of three different proteins as a function of dose is examined at 278 and 100 K.
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Bragg coherent diffraction imaging and metrics for radiation damage in protein micro-crystallography
A combination of Bragg coherent diffractive imaging and reciprocal-space mapping results indicate that the global radiation damage behaviour of micro-crystals is different compared with macroscale crystals.
research papers
A prototype split-and-delay unit (SDU) for XFEL pulses was designed based on the Graeff–Bonse four-Bragg-reflection interferometer by installing 12.5° slopes and evaluated by synchrotron radiation X-rays. The ease of the tunability of the exact delay time across 0 fs by the present SDU was demonstrated.
One-dimensional single-crystal diamond refractive lenses of novel design were produced by laser ablation. They were tested using an X-ray focusing mode, Talbot interferometry, X-ray radiography and X-ray topography.
A comprehensive model of the Imaging and Medical Beamline at the Australian Synchrotron has been developed, validated against a variety of experimental measurements, and its versatility, reliability and robustness demonstrated. The results presented are of particular relevance in X-ray imaging, tomography, radiotherapy and dosimetry.
Generation of apodized X-ray illumination and its application to scanning and diffraction microscopy
Apodized X-ray illumination generated by a two-stage deformable Kirkpatrick–Baez mirror system was employed to improve the image quality in scanning X-ray fluorescence microscopy. It is also demonstrated that the apodized X-ray illumination enables non-isolated objects to be imaged by coherent X-ray diffractive imaging in a non-scanning mode.
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An X-ray grating interferometry setup for wavefront metrology measurements at synchrotron and X-ray free-electron laser facilities and exemplary measurements are reported.
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A bunch-by-bunch measurement system has been developed at Pohang Light Source II, consisting of a four-channel button pick-up, 20 GHz sampling oscilloscope and an 800 MHz low-pass digital filter.
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A multilayer-based collimated plane-grating monochromator (cPGM) with efficiency one order of magnitude higher than the traditional cPGM is proposed for the tender X-ray range. The resolving power can also be increased with improved photon flux by using a large blaze angle and working at high diffraction order.
The experimental uncertainties concerning electron spin polarization under various realistic measurement conditionse are theoretically derived. Supported by numerical simulations, these results define new mathematical instruments for handling the correct statistics of spin polarization measurements in the presence of source intensity fluctuations and are applied to the characteristics of a wide set of state-of-the-art facilities.
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A supervised learning approach for dynamic sampling was found to enable reconstruction of protein crystal position with a significant reduction in both the total X-ray exposure of the sample and to the exposure to the interior of the crystal.
Online metrology of beamline specifications is important but often sacrificed for reasons of time constraints. A technique that permits a reliable metrology without interruption of the measurement workflow is presented.
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Efficient strategies to perform iterative reconstruction of underconstrained datasets in full interior tomography are presented.
A flat-field correction method is proposed for X-ray computed tomography using the edges of the sinogram (not shadowed by the sample) to adjust the best suited combination of flat-fields.
Synchrotron-radiation-based phase-contrast imaging of soybean leaves grown from magneto-primed seeds is presented.
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The development of new sets-ups for tomography measurements under extreme conditions of pressure and temperature at synchrotron sources is reported.
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Multimodal chemical tomography is a technique that has to deal with a variety of big (>100 GB) datasets. Here, a novel method for approaching the analysis of such data using a Python-based big data solution is presented.
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A method for reducing the cupping effect in local tomography based on a known region is proposed.
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Spatially resolved signal collection enhances data quality of non-resonant inelastic X-ray scattering experiments dramatically. This new technique is demonstrated by presenting data from the O K- and Si L2,3-edge of SiO2 α-quartz at high pressure.
Limitations arise for the pressure range where high quality data can be recorded with X-ray Raman scattering spectroscopy. To overcome such issues, miniature diamond anvils of less than 500 µm thickness that can sustain pressure of 70 GPa with large opening enabling high- and low-angle scattering geometry have been developed. On beamline ID20 at the ESRF, data of unprecedented quality were collected on the silicon L-edge and oxygen K-edge in SiO2 glass up to 47 GPa.
The angular distribution of the total reflection X-ray fluorescence signal can suggest a distribution of particle heights deposited on a surface. This height distribution can be deduced by fitting theoretical concentration profiles representative of particles.
The study of multilayer stacks (e.g. thin-film solar cells) by X-ray fluorescence requires a thorough account of the depth-dependent attenuation of incident and excident X-ray beam intensity, as well as spatial thickness variations to achieve an accurate interpretation of the data. A procedure is presented that allows for the assessment of stoichiometric composition variations in high spatial resolution imaging by correcting for multiple effects.
An investigation into when RIXS measurements bring extra information compared with XAS is presented. Two models are used to analyse the RIXS data: an exciton model and a continuum model, which describe the quadrupole and dipole excitations, respectively.
A novel experimental setup is presented for resonant inelastic X-ray scattering investigations of solid and liquid samples in the soft X-ray region for studying the complex electronic configuration of (bio)chemical systems. The uniqueness of the apparatus is its high flexibility combined with optimal energy resolution and energy range ratio.
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To find the ideal synchrotron radiation induced imaging method for the investigation of trace element distributions in bone tissue, experiments with a scanning confocal micro X-ray fluorescence system and a full-field color X-ray camera setup were performed.
Analytic formulas for the angular and the spectral fluxes of a Compton source are established according to the Compton kinematics and to the characteristics of the incoming electron and laser beams. These analytic expressions allow one to compute easily and precisely the X-ray flux in a given angular acceptance and a given energy bandwidth.
beamlines
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The P13 macromolecular crystallography beamline, based on the low-emittance source PETRA III, enables X-ray diffraction experiments on macromolecular crystals over a wide wavelength range (0.7–3.1 Å). The beam has a variable focus size and a small divergence enabling data collection on micrometre-sized crystals.
The microprobe station of the SXRMB is described. A set of Kirkpatrick–Baez mirrors is used to focus the beam to a 10 µm × 10 µm spot. The beamline covers a photon energy range of 1.7–10 keV and it is optimized for several not-easily accessible elements such as Si, P and S.
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The protein crystallography beamline BL2S1 has been constructed on the 5 T superbend port of the AichiSR.
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SPECIES, the soft X-ray beamline for resonant inelastic scattering and ambient-pressure photoelectron spectroscopy at MAX IV, is described.
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The Photo-Emission and Atomic Resolution Laboratory is a new soft X-ray beamline at the Swiss Light Source for the study of surface structure using photoelectron diffraction and scanning tunneling microscopy.
computer programs
An open-source Labview-based program for automatic on-line beamline optimization using an evolutionary algorithm is reported.
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