Literature DB >> 12777808

Zero-dose extrapolation as part of macromolecular synchrotron data reduction.

Kay Diederichs1, Sean McSweeney, Raimond B G Ravelli.   

Abstract

Radiation damage to macromolecular crystals at third-generation synchrotron sites constitutes a major source of systematic error in X-ray data collection. Here, a computational method to partially correct the observed intensities during data reduction is described and investigated. The method consists of a redundancy-based zero-dose extrapolation of a decay function that is fitted to the intensities of all observations of a unique reflection as a function of dose. It is shown in a test case with weak anomalous signal that this conceptually simple correction, when applied to each unique reflection, can significantly improve the accuracy of averaged intensities and single-wavelength anomalous dispersion phases and leads to enhanced experimental electron-density maps. Limitations of and possible improvements to the method are discussed.

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Year:  2003        PMID: 12777808     DOI: 10.1107/s0907444903006516

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  36 in total

1.  Role of insert-1 of myosin VI in modulating nucleotide affinity.

Authors:  Olena Pylypenko; Lin Song; Gaelle Squires; Xiaoyan Liu; Alan B Zong; Anne Houdusse; H Lee Sweeney
Journal:  J Biol Chem       Date:  2011-01-29       Impact factor: 5.157

2.  Experimental approaches to kinetics of gas diffusion in hydrogenase.

Authors:  Fanny Leroux; Sébastien Dementin; Bénédicte Burlat; Laurent Cournac; Anne Volbeda; Stéphanie Champ; Lydie Martin; Bruno Guigliarelli; Patrick Bertrand; Juan Fontecilla-Camps; Marc Rousset; Christophe Léger
Journal:  Proc Natl Acad Sci U S A       Date:  2008-08-06       Impact factor: 11.205

3.  XDS.

Authors:  Wolfgang Kabsch
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

4.  Identification of patterns in diffraction intensities affected by radiation exposure.

Authors:  Dominika Borek; Zbigniew Dauter; Zbyszek Otwinowski
Journal:  J Synchrotron Radiat       Date:  2012-12-06       Impact factor: 2.616

5.  Objective evaluation of radiation damage in a nucleoprotein complex.

Authors:  Zbigniew Dauter
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-04-28       Impact factor: 7.652

6.  Radiation damage in protein crystals is reduced with a micron-sized X-ray beam.

Authors:  Ruslan Sanishvili; Derek W Yoder; Sudhir Babu Pothineni; Gerd Rosenbaum; Shenglan Xu; Stefan Vogt; Sergey Stepanov; Oleg A Makarov; Stephen Corcoran; Richard Benn; Venugopalan Nagarajan; Janet L Smith; Robert F Fischetti
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-28       Impact factor: 11.205

7.  Radiation damage in macromolecular crystallography: what is it and why should we care?

Authors:  Elspeth F Garman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

8.  Diffraction data analysis in the presence of radiation damage.

Authors:  Dominika Borek; Marcin Cymborowski; Mischa Machius; Wladek Minor; Zbyszek Otwinowski
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

9.  Developments in low-resolution biological X-ray crystallography.

Authors:  Fred Dyda
Journal:  F1000 Biol Rep       Date:  2010-11-11

10.  Myosin VI deafness mutation prevents the initiation of processive runs on actin.

Authors:  Olena Pylypenko; Lin Song; Ai Shima; Zhaohui Yang; Anne M Houdusse; H Lee Sweeney
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-06       Impact factor: 11.205

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