Literature DB >> 24297937

Predicting the X-ray lifetime of protein crystals.

Oliver B Zeldin1, Sandor Brockhauser, John Bremridge, James M Holton, Elspeth F Garman.   

Abstract

Radiation damage is a major cause of failure in macromolecular crystallography experiments. Although it is always best to evenly illuminate the entire volume of a homogeneously diffracting crystal, limitations of the available equipment and imperfections in the sample often require a more sophisticated targeting strategy, involving microbeams smaller than the crystal, and translations of the crystal during data collection. This leads to a highly inhomogeneous distribution of absorbed X-rays (i.e., dose). Under these common experimental conditions, the relationship between dose and time is nonlinear, making it difficult to design an experimental strategy that optimizes the radiation damage lifetime of the crystal, or to assign appropriate dose values to an experiment. We present, and experimentally validate, a predictive metric diffraction-weighted dose for modeling the rate of decay of total diffracted intensity from protein crystals in macromolecular crystallography, and hence we can now assign appropriate "dose" values to modern experimental setups. Further, by taking the ratio of total elastic scattering to diffraction-weighted dose, we show that it is possible to directly compare potential data-collection strategies to optimize the diffraction for a given level of damage under specific experimental conditions. As an example of the applicability of this method, we demonstrate that by offsetting the rotation axis from the beam axis by 1.25 times the full-width half maximum of the beam, it is possible to significantly extend the dose lifetime of the crystal, leading to a higher number of diffracted photons, better statistics, and lower overall radiation damage.

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Year:  2013        PMID: 24297937      PMCID: PMC3870734          DOI: 10.1073/pnas.1315879110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  22 in total

1.  Absorbed dose calculations for macromolecular crystals: improvements to RADDOSE.

Authors:  Karthik S Paithankar; Robin Leslie Owen; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2009-02-25       Impact factor: 2.616

2.  Quantifying X-ray radiation damage in protein crystals at cryogenic temperatures.

Authors:  Jan Kmetko; Naji S Husseini; Matthew Naides; Yevgeniy Kalinin; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-08-19

3.  Optimizing the spatial distribution of dose in X-ray macromolecular crystallography.

Authors:  Oliver B Zeldin; Markus Gerstel; Elspeth F Garman
Journal:  J Synchrotron Radiat       Date:  2012-11-29       Impact factor: 2.616

4.  Know your dose: RADDOSE.

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

5.  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

6.  Radiation damage in protein serial femtosecond crystallography using an x-ray free-electron laser.

Authors:  Lukas Lomb; Thomas R M Barends; Stephan Kassemeyer; Andrew Aquila; Sascha W Epp; Benjamin Erk; Lutz Foucar; Robert Hartmann; Benedikt Rudek; Daniel Rolles; Artem Rudenko; Robert L Shoeman; Jakob Andreasson; Sasa Bajt; Miriam Barthelmess; Anton Barty; Michael J Bogan; Christoph Bostedt; John D Bozek; Carl Caleman; Ryan Coffee; Nicola Coppola; Daniel P Deponte; R Bruce Doak; Tomas Ekeberg; Holger Fleckenstein; Petra Fromme; Maike Gebhardt; Heinz Graafsma; Lars Gumprecht; Christina Y Hampton; Andreas Hartmann; Günter Hauser; Helmut Hirsemann; Peter Holl; James M Holton; Mark S Hunter; Wolfgang Kabsch; Nils Kimmel; Richard A Kirian; Mengning Liang; Filipe R N C Maia; Anton Meinhart; Stefano Marchesini; Andrew V Martin; Karol Nass; Christian Reich; Joachim Schulz; M Marvin Seibert; Raymond Sierra; Heike Soltau; John C H Spence; Jan Steinbrener; Francesco Stellato; Stephan Stern; Nicusor Timneanu; Xiaoyu Wang; Georg Weidenspointner; Uwe Weierstall; Thomas A White; Cornelia Wunderer; Henry N Chapman; Joachim Ullrich; Lothar Strüder; Ilme Schlichting
Journal:  Phys Rev B Condens Matter Mater Phys       Date:  2011-12-01

Review 7.  Scaling and assessment of data quality.

Authors:  Philip Evans
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-12-14

8.  Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF.

Authors:  Stéphanie Monaco; Elspeth Gordon; Matthew W Bowler; Solange Delagenière; Matias Guijarro; Darren Spruce; Olof Svensson; Sean M McSweeney; Andrew A McCarthy; Gordon Leonard; Max H Nanao
Journal:  J Appl Crystallogr       Date:  2013-05-15       Impact factor: 3.304

9.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

10.  A survey of global radiation damage to 15 different protein crystal types at room temperature: a new decay model.

Authors:  Ricardo Miguel Ferraz Leal; Gleb Bourenkov; Silvia Russi; Alexander N Popov
Journal:  J Synchrotron Radiat       Date:  2012-12-06       Impact factor: 2.616

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  35 in total

1.  Radiation decay of thaumatin crystals at three X-ray energies.

Authors:  Dorothee Liebschner; Gerold Rosenbaum; Miroslawa Dauter; Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-03-26

2.  Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources.

Authors:  Pierre Aller; Allen M Orville
Journal:  Methods Mol Biol       Date:  2021

Review 3.  E pluribus unum, no more: from one crystal, many conformations.

Authors:  Rahel A Woldeyes; David A Sivak; James S Fraser
Journal:  Curr Opin Struct Biol       Date:  2014-08-09       Impact factor: 6.809

Review 4.  Crystallographic phasing from weak anomalous signals.

Authors:  Qun Liu; Wayne A Hendrickson
Journal:  Curr Opin Struct Biol       Date:  2015-09-30       Impact factor: 6.809

5.  Estimate your dose: RADDOSE-3D.

Authors:  Charles S Bury; Jonathan C Brooks-Bartlett; Steven P Walsh; Elspeth F Garman
Journal:  Protein Sci       Date:  2017-11-06       Impact factor: 6.725

6.  Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation.

Authors:  Henry van den Bedem; Mark A Wilson
Journal:  J Synchrotron Radiat       Date:  2019-06-13       Impact factor: 2.616

7.  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

Review 8.  Assessing and maximizing data quality in macromolecular crystallography.

Authors:  P Andrew Karplus; Kay Diederichs
Journal:  Curr Opin Struct Biol       Date:  2015-07-24       Impact factor: 6.809

9.  Evaluating the impact of X-ray damage on conformational heterogeneity in room-temperature (277 K) and cryo-cooled protein crystals.

Authors:  Filip Yabukarski; Tzanko Doukov; Daniel A Mokhtari; Siyuan Du; Daniel Herschlag
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-14       Impact factor: 5.699

10.  Serial macromolecular crystallography at ALBA Synchrotron Light Source.

Authors:  Jose M Martin-Garcia; Sabine Botha; Hao Hu; Rebecca Jernigan; Albert Castellví; Stella Lisova; Fernando Gil; Barbara Calisto; Isidro Crespo; Shatabdi Roy-Chowdhury; Alice Grieco; Gihan Ketawala; Uwe Weierstall; John Spence; Petra Fromme; Nadia Zatsepin; Dirk Roeland Boer; Xavi Carpena
Journal:  J Synchrotron Radiat       Date:  2022-04-04       Impact factor: 2.557

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