Journal of Synchrotron Radiation

Volume 18, Part 3 (May 2011)


Includes papers presented at the Sixth International Workshop on X-ray Radiation Damage to Biological Crystalline Samples

SLAC National Accelerator Laboratory, Menlo Park, CA, USA, 11-13 March 2010

[Buy print version] A printed copy of this issue is available for purchase


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Upper panel: X-ray dose-dependent preferential reduction of a nitrate ion in the vicinity of the Cys6-Cys127 disulfide bond of chicken egg-white lysozyme (see De la Mora, Carmichael and Garman, pages 346-357). Lower panel: electron dose-dependent snapshots of a radiation damage series consisting of successive cryo-electron microscopy images of individual molecules of extracellular hemoglobin (see Karuppasamy, Nejadasl, Vulovic, Koster and Ravelli, pages 398-412). These pieces of research, among others, were presented at the 6th International Workshop on X-ray Radiation Damage to Biological Crystalline Samples (RD6) that took place on 11-13 March 2010 at the Stanford Synchrotron Radiation Lightsource in California, USA.

radiation damage


 

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J. Synchrotron Rad. (2011). 18, 313-317  [ doi:10.1107/S0909049511013859 ]

Macromolecular crystallography radiation damage research: what's new?

E. F. Garman and M. Weik

Synopsis: An introductory overview of the special issue papers on radiation damage in this issue..

Online 27 April 2011


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J. Synchrotron Rad. (2011). 18, 318-328  [ doi:10.1107/S090904951100968X ]

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

C. Rajendran, F. S. N. Dworkowski, M. Wang and C. Schulze-Briese

Synopsis: Observations of the dose-rate effect in continuous X-ray diffraction data acquisition at room temperature are presented.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 329-337  [ doi:10.1107/S0909049511007631 ]

Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin

D. H. Juers and M. Weik

Synopsis: In a protein crystal an increase in the atomic B-factor after radiation exposure at 160 K correlates with the proximity to solvent channels.

PDB references: 3p7p, 3p7q, 3p7r, 3p7s, 3p7t, 3p7u, 3p7v and 3p7w

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 338-345  [ doi:10.1107/S0909049511005504 ]

Energy dependence of site-specific radiation damage in protein crystals

C. Homer, L. Cooper and A. Gonzalez

Synopsis: The energy dependence of specific radiation damage to sulfur sites in tetragonal HEWL lysozyme is studied.

Online 15 March 2011


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J. Synchrotron Rad. (2011). 18, 346-357  [ doi:10.1107/S0909049511007163 ]

Effective scavenging at cryotemperatures: further increasing the dose tolerance of protein crystals

E. De la Mora, I. Carmichael and E. F. Garman

Synopsis: Sodium nitrate, an electron scavenger, is shown to be an effective agent in reducing the rate of global radiation damage with increasing dose, and to be even more effective in quenching specific structural damage in native HEWL crystals at 100 K.

Online 1 April 2011


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J. Synchrotron Rad. (2011). 18, 358-366  [ doi:10.1107/S0909049511006315 ]

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

A. M. Orville, R. Buono, M. Cowan, A. Héroux, G. Shea-McCarthy, D. K. Schneider, J. M. Skinner, M. J. Skinner, D. Stoner-Ma and R. M. Sweet

Synopsis: The instrumentation and methods available for collecting almost simultaneous single-crystal electronic absorption correlated with X-ray diffraction data at NSLS beamline X26-C are reviewed, as well as a very brief outline of its Raman spectroscopy capability.

Online 19 March 2011


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J. Synchrotron Rad. (2011). 18, 367-373  [ doi:10.1107/S0909049511004250 ]

Revealing low-dose radiation damage using single-crystal spectroscopy

R. L. Owen, B. A. Yorke, J. A. Gowdy and A. R. Pearson

Synopsis: Data on the rapid reduction of haem proteins in the X-ray beam at synchrotron sources are presented. The use of single-crystal spectroscopy to detect these changes and their implication for diffraction data collection from oxidized species is also discussed.

Online 19 March 2011


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J. Synchrotron Rad. (2011). 18, 374-380  [ doi:10.1107/S0909049511004092 ]

Additional phase information from UV damage of selenomethionine labelled proteins

D. de Sanctis, P. A. Tucker and S. Panjikar

Synopsis: Successful examples of ultraviolet radiation-damage-induced phasing with anomalous scattering from selenomethionine protein crystals have been demonstrated.

Online 11 March 2011


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J. Synchrotron Rad. (2011). 18, 381-386  [ doi:10.1107/S0909049511002251 ]

Experimental procedure for the characterization of radiation damage in macromolecular crystals

R. M. F. Leal, G. P. Bourenkov, O. Svensson, D. Spruce, M. Guijarro and A. N. Popov

Synopsis: A novel automatic procedure to determine the sensitivity of macromolecular crystals to radiation damage is presented. The information extracted from this procedure can be directly used for optimal planning of data collection or/and beamline calibration.

Online 10 March 2011


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J. Synchrotron Rad. (2011). 18, 387-397  [ doi:10.1107/S0909049511008235 ]

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

T. Krojer and F. von Delft

Synopsis: A retrospective analysis of radiation damage behaviour in a statistically significant number of real-life datasets is presented, in order to gauge the importance of the complications not yet measured or rigorously evaluated in current experiments, and the challenges that remain before radiation damage can be considered a problem solved in practice.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 398-412  [ doi:10.1107/S090904951100820X ]

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

M. Karuppasamy, F. Karimi Nejadasl, M. Vulovic, A. J. Koster and R. B. G. Ravelli

Synopsis: The effects of dose and dose-rate were investigated for single-particle cryo-electron microscopy using stroboscopic data collection. A dose-rate effect was observed favoring lower flux densities.

Online 9 April 2011


research papers


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J. Synchrotron Rad. (2011). 18, 413-417  [ doi:10.1107/S0909049511003190 ]

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

T. W. Cornelius, D. Carbone, V. L. R. Jacques, T. U. Schülli and T. H. Metzger

Synopsis: 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.

Online 15 March 2011


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J. Synchrotron Rad. (2011). 18, 418-426  [ doi:10.1107/S0909049511002949 ]

Quantitative local structure determination in mica crystals: ab initio simulations of polarization XANES at the potassium K-edge

W. Xu, D. Chen, W. Chu, Z. Wu, A. Marcelli, A. Mottana, A. Soldatov and M. F. Brigatti

Synopsis: Angle-resolved XANES at the potassium K-edge and single-crystal X-ray diffraction experiments are combined to characterize structural distortions and compositional disorder of micas. Full-multiple-scattering XANES analysis is presented and limitations of the muffin-tin potential in layered systems are discussed.

Online 10 March 2011


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J. Synchrotron Rad. (2011). 18, 427-435  [ doi:10.1107/S0909049511006005 ]

Suppression of ring artefacts when tomographing anisotropically attenuating samples

S. Titarenko, V. Titarenko, A. Kyrieleis, P. Withers and F. De Carlo

Synopsis: An intensity normalization technique is proposed to suppress ring artefacts of varying strength. The method was applied to an elongated sample in a monochromatic beam and to a sample with highly attenuated parts in a white beam.

Online 2 April 2011


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J. Synchrotron Rad. (2011). 18, 436-441  [ doi:10.1107/S0909049511004031 ]

Reconstruction of electron beam distribution using phase-retrieval algorithm

Y. W. Parc, C. Kim, J. Y. Huang and I. S. Ko

Synopsis: The transverse distribution of an electron beam in a storage ring can be reconstructed by using a phase-retrieval algorithm.

Online 11 March 2011


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J. Synchrotron Rad. (2011). 18, 442-446  [ doi:10.1107/S0909049511002366 ]

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

S. Gorelick, J. Vila-Comamala, V. A. Guzenko, R. Barrett, M. Salomé and C. David

Synopsis: The efficiencies of several Fresnel zone plates, that were fabricated using a direct-write method with high-energy electrons, were measured over a wide range of photon energies.

Online 10 March 2011


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J. Synchrotron Rad. (2011). 18, 447-455  [ doi:10.1107/S0909049511005802 ]

In situ diffuse reflectance IR spectroscopy and X-ray absorption spectroscopy for fast catalytic processes

N. S. Marinkovic, Q. Wang and A. I. Frenkel

Synopsis: A new instrument for synchronous in situ investigations by infrared and X-ray absorption spectroscopies was designed and built at the Synchrotron Catalysis Consortium, NSLS, Brookhaven National Laboratory. It combines two complementary methods, DRIFTS and XAFS, for solving electronic, structural and kinetic problems for a wide range of catalysts, reactive conditions and time scales.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 456-463  [ doi:10.1107/S0909049511006017 ]

Specific molecular and cellular events induced by irradiated X-ray photoactivatable drugs raise the problem of co-toxicities: particular consequences for anti-cancer synchrotron therapy

J. Gastaldo, Z. Bencokova, C. Massart, A. Joubert, J. Balosso, A.-M. Charvet and N. Foray

Synopsis: X-ray photoactivatable drugs and co-toxicities: consequences for synchrotron radiotherapy.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 464-474  [ doi:10.1107/S0909049511002640 ]

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

S. T. Kelly, J. C. Trenkle, L. J. Koerner, S. C. Barron, N. Walker, P. O. Pouliquen, M. W. Tate, S. M. Gruner, E. M. Dufresne, T. P. Weihs and T. Hufnagel

Synopsis: Techniques are described for X-ray diffraction combining micrometer-scale spatial resolution with microsecond-scale temporal resolution for studying rapid localized irreversible transformations in materials.

Online 16 March 2011


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J. Synchrotron Rad. (2011). 18, 475-480  [ doi:10.1107/S0909049511006984 ]

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

C. Nguyen, H. K. Ea, D. Thiaudiere, S. Reguer, D. Hannouche, M. Daudon, F. Lioté and D. Bazin

Synopsis: X-ray absorption near-edge structure spectroscopy has been used to accurately characterize sparse calcium-containing crystals in human OA cartilage.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 481-491  [ doi:10.1107/S0909049511004511 ]

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

W. Roseker, H. Franz, H. Schulte-Schrepping, A. Ehnes, O. Leupold, F. Zontone, S. Lee, A. Robert and G. Grübel

Synopsis: A prototype device capable of splitting an X-ray pulse into two adjustable fractions, delaying one of them with the aim of performing split pulse X-ray photon correlation spectroscopy and pump-probe type studies was designed and manufactured. Time delays up to 2.95 ns have been demonstrated. The achieved contrast values of 56% indicate a feasibility of performing coherence-based experiments with the delay line.

Online 19 March 2011


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J. Synchrotron Rad. (2011). 18, 492-496  [ doi:10.1107/S0909049511001828 ]

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

A. H. Said, H. Sinn and R. Divan

Synopsis: New improvements related to the fabrication of spherical bent analyzers for 1 meV energy-resolution inelastic X-ray scattering spectroscopy are presented.

Online 10 March 2011


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J. Synchrotron Rad. (2011). 18, 497-505  [ doi:10.1107/S0909049511009071 ]

High-resolution stress mapping of polycrystalline alumina compression using synchrotron X-ray diffraction

S. Raghavan and P. Imbrie

Synopsis: High-energy X-rays were used to capture powder diffraction profiles over a half-section of a polycrystalline alumina parallelepiped sample under an increasing uniaxial compressive load. The data was converted to strain and results were used for stress mapping of the sample.

Online 9 April 2011


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J. Synchrotron Rad. (2011). 18, 506-514  [ doi:10.1107/S0909049511005796 ]

In situ powder diffraction study of belite sulfoaluminate clinkering

Á. G. De la Torre, A. J. M. Cuberos, G. Álvarez-Pinazo, A. Cuesta and M. A. G. Aranda

Synopsis: Clinkering reactions and processes have been established for belite sulfoaluminate cements by high-energy synchrotron powder diffraction at high temperatures.

Online 15 March 2011


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J. Synchrotron Rad. (2011). 18, 515-521  [ doi:10.1107/S0909049511008624 ]

Geometrical layout and optics modelling of the surface science beamline station at the SESAME synchrotron radiation facility

W. Salah and M. Sanchez del Rio

Synopsis: A quantitative analysis and computer modelling of the surface science beamline station D09 at the SESAME synchrotron radiation facility are presented.

Online 19 March 2011


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J. Synchrotron Rad. (2011). 18, 522-526  [ doi:10.1107/S0909049511009083 ]

X-ray collimation by crystals with precise parabolic holes based on diffractive-refractive optics

P. Oberta, P. Mikulík, M. Kittler and J. Hrdý

Synopsis: X-ray collimation as a novel application of diffractive-refractive optics was studied theoretically and experimentally. A set-up with two crystals in a dispersive arrangement successfully demonstrated X-ray collimation in the energy range 6.3-18.8 keV.

Online 1 April 2011


short communications


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J. Synchrotron Rad. (2011). 18, 527-529  [ doi:10.1107/S090904951100344X ]

Use of Soller slits to remove reference foil fluorescence from transmission spectra

J. J. Tse, G. N. George and I. J. Pickering

Synopsis: Use of Soller slits to remove back-fluorescence from the reference foil helps provide more accurate transmission X-ray absorption spectra of weak samples.

Online 19 March 2011


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J. Synchrotron Rad. (2011). 18, 530-533  [ doi:10.1107/S0909049511002627 ]

Synchrotron-radiation-induced oxidation of selenite to selenate in coal-derived fly ash

F. E. Huggins and H. Sanei

Synopsis: Based on variations observed in successive Se XAFS scans of a coal-derived fly-ash, 15-20% of the selenite in the fly-ash is estimated to have oxidized to selenate as a result of exposure to synchrotron radiation for 2 h.

Online 11 March 2011


current events


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J. Synchrotron Rad. (2011). 18, 534-536  [ doi:10.1107/S0909049511012805 ]

Current events

Online 8 April 2011


 

J. Synchrotron Rad. (2011). 18, 537

forthcoming meetings and short courses


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