Literature DB >> 28921782

Estimate your dose: RADDOSE-3D.

Charles S Bury1, Jonathan C Brooks-Bartlett1, Steven P Walsh1, Elspeth F Garman1.   

Abstract

We present the current status of RADDOSE-3D, a software tool allowing the estimation of the dose absorbed in a macromolecular crystallography diffraction experiment. The code allows a temporal and spatial dose contour map to be calculated for a crystal of any geometry and size as it is rotated in an X-ray beam, and gives several summary dose values: among them diffraction weighted dose. This allows experimenters to plan data collections which will minimize radiation damage effects by spreading the absorbed dose more homogeneously, and thus to optimize the use of their crystals. It also allows quantitative comparisons between different radiation damage studies, giving a universal "x-axis" against which to plot various metrics.
© 2017 The Protein Society.

Keywords:  absorption coefficients; beam profile; diffraction weighted dose; dose; radiation damage

Mesh：

Year:  2017        PMID： 28921782      PMCID： PMC5734275          DOI： 10.1002/pro.3302

Source DB:  PubMed          Journal:  Protein Sci        ISSN： 0961-8368            Impact factor:   6.725


  35 in total

Review 1.  Physical and chemical considerations of damage induced in protein crystals by synchrotron radiation: a radiation chemical perspective.

Authors:  Peter O'Neill; David L Stevens; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2002-11-01       Impact factor: 2.616

2.  Unit-cell volume change as a metric of radiation damage in crystals of macromolecules.

Authors:  Raimond B G Ravelli; Pascal Theveneau; Sean McSweeney; Martin Caffrey
Journal:  J Synchrotron Radiat       Date:  2002-11-01       Impact factor: 2.616

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

Authors:  Eugenio De la Mora; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2011-04-01       Impact factor: 2.616

4.  Optimization of data collection taking radiation damage into account.

Authors:  Gleb P Bourenkov; Alexander N Popov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

5.  Know your dose: RADDOSE.

Authors:  Karthik S Paithankar; Elspeth F Garman
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

6.  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

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

Authors:  Adam I Barker; Robert J Southworth-Davies; Karthik S Paithankar; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2009-02-25       Impact factor: 2.616

8.  Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

Authors:  Sam Horrell; Svetlana V Antonyuk; Robert R Eady; S Samar Hasnain; Michael A Hough; Richard W Strange
Journal:  IUCrJ       Date:  2016-06-15       Impact factor: 4.769

9.  Development of tools to automate quantitative analysis of radiation damage in SAXS experiments.

Authors:  Jonathan C Brooks-Bartlett; Rebecca A Batters; Charles S Bury; Edward D Lowe; Helen Mary Ginn; Adam Round; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2017-01-01       Impact factor: 2.616

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

Authors:  Elizabeth G Allan; Melissa C Kander; Ian Carmichael; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2012-12-05       Impact factor: 2.616
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  32 in total

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Authors:  Vivek Srinivas; Rahul Banerjee; Hugo Lebrette; Jason C Jones; Oskar Aurelius; In-Sik Kim; Cindy C Pham; Sheraz Gul; Kyle D Sutherlin; Asmit Bhowmick; Juliane John; Esra Bozkurt; Thomas Fransson; Pierre Aller; Agata Butryn; Isabel Bogacz; Philipp Simon; Stephen Keable; Alexander Britz; Kensuke Tono; Kyung Sook Kim; Sang-Youn Park; Sang Jae Lee; Jaehyun Park; Roberto Alonso-Mori; Franklin D Fuller; Alexander Batyuk; Aaron S Brewster; Uwe Bergmann; Nicholas K Sauter; Allen M Orville; Vittal K Yachandra; Junko Yano; John D Lipscomb; Jan Kern; Martin Högbom
Journal:  J Am Chem Soc       Date:  2020-08-05       Impact factor: 15.419

3.  Non-Contact Universal Sample Presentation for Room Temperature Macromolecular Crystallography Using Acoustic Levitation.

Authors:  R H Morris; E R Dye; D Axford; M I Newton; J H Beale; P T Docker
Journal:  Sci Rep       Date:  2019-08-27       Impact factor: 4.379

4.  Structural knowledge or X-ray damage? A case study on xylose isomerase illustrating both.

Authors:  Helena Taberman; Charles S Bury; Mark J van der Woerd; Edward H Snell; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2019-06-24       Impact factor: 2.616

5.  Crystallographic Studies of Rhodopsins: Structure and Dynamics.

Authors:  Marie Luise Grünbein; Gabriela Nass Kovacs; Marco Kloos; Alexander Gorel; R Bruce Doak; Robert L Shoeman; Thomas R M Barends; Ilme Schlichting
Journal:  Methods Mol Biol       Date:  2022

6.  Native SAD phasing at room temperature.

Authors:  Jack B Greisman; Kevin M Dalton; Candice J Sheehan; Margaret A Klureza; Igor Kurinov; Doeke R Hekstra
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-27       Impact factor: 5.699

7.  The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature.

Authors:  Galen J Correy; Daniel W Kneller; Gwyndalyn Phillips; Swati Pant; Silvia Russi; Aina E Cohen; George Meigs; James M Holton; Stefan Gahbauer; Michael C Thompson; Alan Ashworth; Leighton Coates; Andrey Kovalevsky; Flora Meilleur; James S Fraser
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8.  Anaerobic fixed-target serial crystallography.

Authors:  Patrick Rabe; John H Beale; Agata Butryn; Pierre Aller; Anna Dirr; Pauline A Lang; Danny N Axford; Stephen B Carr; Thomas M Leissing; Michael A McDonough; Bradley Davy; Ali Ebrahim; Julien Orlans; Selina L S Storm; Allen M Orville; Christopher J Schofield; Robin L Owen
Journal:  IUCrJ       Date:  2020-08-21       Impact factor: 4.769

9.  Instrumentation and experimental procedures for robust collection of X-ray diffraction data from protein crystals across physiological temperatures.

Authors:  Tzanko Doukov; Daniel Herschlag; Filip Yabukarski
Journal:  J Appl Crystallogr       Date:  2020-11-05       Impact factor: 3.304

10.  Polyimide mesh-based sample holder with irregular crystal mounting holes for fixed-target serial crystallography.

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Journal:  Sci Rep       Date:  2021-06-23       Impact factor: 4.379
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