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Journal of Synchrotron Radiation

Volume 16, Part 2 (March 2009)


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

Villigen, Switzerland, 3-5 March 2008

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


[Issue Author Index][Volume Author Index]
[Cover illustration] Cover illustration: Medical imaging and X-ray crystallography have one thing in common: striking a balance between data quality and radiation damage. James Holton (pictured) discusses how to best reach this compromise in X-ray crystallography (pages 133-142). He was not asked to discuss the same for medical imaging as his skills in this technique (as well as his skill at walking on icy pavements) were deemed questionable based on this image. The Swiss medical services near the Swiss Light Source are thanked for assistance in obtaining this image during the radiation damage meeting.

radiation damage


 

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J. Synchrotron Rad. (2009). 16, 129-132  [ doi:10.1107/S0909049509005238 ]

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

E. F. Garman and C. Nave

Synopsis: The current understanding of radiation damage in protein crystals is reviewed.

Online 25 February 2009


 

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J. Synchrotron Rad. (2009). 16, 133-142  [ doi:10.1107/S0909049509004361 ]

A beginner's guide to radiation damage

J. M. Holton

Synopsis: Radiation damage considerations affecting data collection by more than a factor of two are summarized and damage avoidance strategies are suggested.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 143-151  [ doi:10.1107/S0909049508040429 ]

Determination of X-ray flux using silicon pin diodes

R. L. Owen, J. M. Holton, C. Schulze-Briese and E. F. Garman

Synopsis: Accurate measurement of photon flux from an X-ray source is a parameter required to calculate the dose absorbed by a sample. The development of a model for determining the photon flux incident on pin diodes, and experiments to test this model, are described for incident energies between 4 and 18 keV used in macromolecular crystallography.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 152-162  [ doi:10.1107/S0909049508040430 ]

Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE

K. S. Paithankar, R. L. Owen and E. F. Garman

Synopsis: The dose absorbed by a macromolecular crystal can be calculated using the program RADDOSE. A new version of this program, in which the probability of X-ray fluorescent escape following photoelectric absorption is included, is presented here with some examples of its application.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 163-172  [ doi:10.1107/S0909049509001629 ]

Colouring cryo-cooled crystals: online microspectrophotometry

J. McGeehan, R. B. G. Ravelli, J. W. Murray, R. L. Owen, F. Cipriani, S. McSweeney, M. Weik and E. F. Garman

Synopsis: A portable and readily aligned online microspectrophotometer that can be easily installed on macromolecular crystallography beamlines is described. It allows measurement of the spectral characteristics of macromolecular crystals prior, during, and after the X-ray diffraction experiment.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 173-182  [ doi:10.1107/S0909049508040120 ]

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

R. L. Owen, A. R. Pearson, A. Meents, P. Boehler, V. Thominet and C. Schulze-Briese

Synopsis: Complementary techniques greatly aid the interpretation of macromolecule structures to yield functional information, and can also help to track radiation-induced changes. A new on-axis spectrometer being integrated into the macromolecular crystallography beamlines of the Swiss Light Source is presented.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 183-190  [ doi:10.1107/S0909049509002192 ]

A new aspect of specific radiation damage: hydrogen abstraction from organic molecules

A. Meents, B. Dittrich and S. Gutmann

Synopsis: Radiation-induced structural changes which can be explained by hydrogen abstraction were observed in a high-resolution X-ray diffraction study on cyclosporine A.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 191-204  [ doi:10.1107/S0909049509003331 ]

Can soaked-in scavengers protect metalloprotein active sites from reduction during data collection?

S. Macedo, M. Pechlaner, W. Schmid, M. Weik, K. Sato, C. Dennison and K. Djinovic-Carugo

Synopsis: UV-Vis microspectrophotometry is used to test the efficacy of selected scavengers in reducing the undesirable photoreduction of the iron and copper centres in myoglobin and azurin, respectively, and X-ray crystallography to assess their capacity of mitigating global and specific radiation damage effects.

Online 25 February 2009


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J. Synchrotron Rad. (2009). 16, 205-216  [ doi:10.1107/S0909049509003343 ]

Room-temperature scavengers for macromolecular crystallography: increased lifetimes and modified dose dependence of the intensity decay

A. I. Barker, R. J. Southworth-Davies, K. S. Paithankar, I. Carmichael and E. F. Garman

Synopsis: Two effective scavengers for room-temperature macromolecular crystallography are identified: ascorbate and 1,4-benzoquinone. Addition of these scavengers changes the usually observed diffraction intensity decay with dose from first order to zeroth order, leading to postulates on radiation damage mechanisms.

Online 25 February 2009


research papers


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J. Synchrotron Rad. (2009). 16, 217-225  [ doi:10.1107/S0909049508040612 ]

Mini-beam collimator enables microcrystallography experiments on standard beamlines

R. F. Fischetti, S. Xu, D. W. Yoder, M. Becker, V. Nagarajan, R. Sanishvili, M. C. Hilgart, S. Stepanov, O. Makarov and J. L. Smith

Synopsis: A `mini-beam' apparatus has been developed that conditions the size of an X-ray beam to 5 µm. The design of the apparatus and the characterization of the focal size and flux are presented.

Online 10 January 2009


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J. Synchrotron Rad. (2009). 16, 226-230  [ doi:10.1107/S0909049508040892 ]

The RATIO method for time-resolved Laue crystallography

P. Coppens, M. Pitak, M. Gembicky, M. Messerschmidt, S. Scheins, J. Benedict, S. Adachi, T. Sato, S. Nozawa, K. Ichiyanagi, M. Chollet and S. Koshihara

Synopsis: A RATIO method for analysis of intensity changes in time-resolved pump-probe Laue diffraction experiments is described.

Online 10 January 2009


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J. Synchrotron Rad. (2009). 16, 231-236  [ doi:10.1107/S0909049508041071 ]

Performance of the micro-PIC gaseous area detector in small-angle X-ray scattering experiments

K. Hattori, K. Tsuchiya, K. Ito, Y. Okada, K. Fujii, H. Kubo, K. Miuchi, M. Takata, T. Tanimori and H. Uekusa

Synopsis: A two-dimensional photon-counting detector based on a micro-pixel gas chamber has demonstrated a dynamic range of >105 and a counting rate of up to 5 MHz.

Online 10 January 2009


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J. Synchrotron Rad. (2009). 16, 237-246  [ doi:10.1107/S0909049508043306 ]

Polycapillary-optics-based micro-XANES and micro-EXAFS at a third-generation bending-magnet beamline

G. Silversmit, B. Vekemans, S. Nikitenko, W. Bras, V. Czhech, G. Zaray, I. Szaloki and L. Vincze

Synopsis: A µ-XAS (µ-XANES and µ-EXAFS) set-up based on a polycapillary half-lens has been successfully tested at a bending-magnet station equipped with a non-fixed-exit monochromator.

Online 16 January 2009


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J. Synchrotron Rad. (2009). 16, 247-259  [ doi:10.1107/S0909049509000211 ]

Phosphorus L2,3-edge XANES: overview of reference compounds

J. Kruse, P. Leinweber, K.-U. Eckhardt, F. Godlinski, Y. Hu and L. Zuin

Synopsis: An overview of phosphorus L2,3-edge XANES spectra of pure reference compounds and geological phosphorus minerals, all measured under consistent experimental conditions, is given. In addition, the effect of radiation damage is shown for three compounds and measures are proposed to reduce it.

Online 16 January 2009


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J. Synchrotron Rad. (2009). 16, 260-263  [ doi:10.1107/S0909049508043161 ]

Dielectric properties of (NH4)2SO4 crystals in the range of electronic excitations

B. Andriyevsky, C. Cobet, A. Patryn and N. Esser

Synopsis: Valence electrons excitations of (NH4)2SO4 crystals have been studied by the spectral ellipsometry method using synchrotron radiation in the photon energy range E < 9.5 eV. Large anomalies of the temperature dependences of dielectric permittivity and intensity of reflected radiation have been found in the temperature range close to the phase transition point between para- and ferroelectric phases.

Online 10 January 2009


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J. Synchrotron Rad. (2009). 16, 264-272  [ doi:10.1107/S0909049509000508 ]

The materials science X-ray beamline BL8 at the DELTA storage ring

D. Lützenkirchen-Hecht, R. Wagner, U. Haake, A. Watenphul and R. Frahm

Synopsis: The instrumentation of the materials science X-ray beamline BL8 at the DELTA storage ring is presented together with its specific features. The first user experiments are also briefly described.

Online 29 January 2009


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J. Synchrotron Rad. (2009). 16, 273-282  [ doi:10.1107/S0909049509001265 ]

A curved image-plate detector system for high-resolution synchrotron X-ray diffraction

P. Sarin, R. P. Haggerty, W. Yoon, M. Knapp, A. Berghaeuser, P. Zschack, E. Karapetrova, N. Yang and W. M. Kriven

Synopsis: A new one-dimensional curved image-plate detector for rapid high-resolution powder X-ray diffraction investigations using synchrotron radiation is presented.

Online 3 February 2009


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J. Synchrotron Rad. (2009). 16, 283-292  [ doi:10.1107/S0909049508043768 ]

High-resolution spectroscopy on an X-ray absorption beamline

J.-L. Hazemann, O. Proux, V. Nassif, H. Palancher, E. Lahera, C. Da Silva, A. Braillard, D. Testemale, M.-A. Diot, I. Alliot, W. Del Net, A. Manceau, F. Gélébart, M. Morand, Q. Dermigny and A. Shukla

Synopsis: A bent-crystal spectrometer has been developed and experiments have been carried out in order to demonstrate the interests of a high-resolution detection system on a classical X-ray absorption beamline.

Online 16 January 2009


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J. Synchrotron Rad. (2009). 16, 293-298  [ doi:10.1107/S0909049509000491 ]

A fast energy-dispersive multi-element detector for X-ray absorption spectroscopy

E. Welter, K. Hansen, C. Reckleben and I. Diehl

Synopsis: The results of X-ray absorption fine-structure experiments which were performed to test the applicability of a monolithic seven-cell silicon drift detector module developed at the Hamburger Synchrotron Strahlungslabor (DESY) for this type of measurement are described.

Online 23 January 2009


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J. Synchrotron Rad. (2009). 16, 299-306  [ doi:10.1107/S0909049509000144 ]

Performance of the far-IR beamline of the 6 MeV tabletop synchrotron light source

Md. Monirul Haque, H. Yamada, A. Moon and M. Yamada

Synopsis: The performance of the far-infrared beamline of the 6 MeV MIRRORCLE-type tabletop synchrotron light source dedicated to far-infrared spectroscopy is presented.

Online 21 January 2009


short communications


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J. Synchrotron Rad. (2009). 16, 307-309  [ doi:10.1107/S0909049509000314 ]

Time-resolved X-ray microscopy of nanoparticle aggregates under oscillatory shear

G. K. Auernhammer, K. Fauth, B. Ullrich, J. Zhao, M. Weigand and D. Vollmer

Synopsis: Shear-induced rearrangement of colloidal aggregates was successfully imaged over time by X-ray microscopy, using a home-developed shear cell inserted into the focus plane. That experimental stimulation devices can be designed to meet the accuracy of X-ray microscopy extends the scope of its applications to dynamical processes.

Online 30 January 2009


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J. Synchrotron Rad. (2009). 16, 310-313  [ doi:10.1107/S0909049508043082 ]

A note on medieval microfabrication: the visualization of a prayer nut by synchrotron-based computer X-ray tomography

P. Reischig, J. Blaas, C. Botha, A. Bravin, L. Porra, C. Nemoz, A. Wallert and J. Dik

Synopsis: This papers describes the study of a medieval prayer nut using synchrotron-based X-ray computed tomography, which revealed the fabrication method of the object.

Online 12 February 2009


current events


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J. Synchrotron Rad. (2009). 16, 314-315  [ doi:10.1107/S0909049509004610 ]

Current events

Online 12 February 2009


 

J. Synchrotron Rad. (2009). 16, 316-

forthcoming meetings and short courses


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