Literature DB >> 25849388

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

Dorothee Liebschner1, Gerold Rosenbaum2, Miroslawa Dauter3, Zbigniew Dauter4.   

Abstract

Radiation damage is an unavoidable obstacle in X-ray crystallographic data collection for macromolecular structure determination, so it is important to know how much radiation a sample can endure before being degraded beyond an acceptable limit. In the literature, the threshold at which the average intensity of all recorded reflections decreases to a certain fraction of the initial value is called the `dose limit'. The first estimated D50 dose-limit value, at which the average diffracted intensity was reduced to 50%, was 20 MGy and was derived from observing sample decay in electron-diffraction experiments. A later X-ray study carried out at 100 K on ferritin protein crystals arrived at a D50 of 43 MGy, and recommended an intensity reduction of protein reflections to 70%, D70, corresponding to an absorbed dose of 30 MGy, as a more appropriate limit for macromolecular crystallography. In the macromolecular crystallography community, the rate of intensity decay with dose was then assumed to be similar for all protein crystals. A series of diffraction images of cryocooled (100 K) thaumatin crystals at identical small, 2° rotation intervals were recorded at X-ray energies of 6.33 , 12.66 and 19.00 keV. Five crystals were used for each wavelength. The decay in the average diffraction intensity to 70% of the initial value, for data extending to 2.45 Å resolution, was determined to be about 7.5 MGy at 6.33 keV and about 11 MGy at the two higher energies.

Entities:  

Keywords:  dose limit; energy dependence; radiation damage

Mesh:

Substances:

Year:  2015        PMID: 25849388      PMCID: PMC4388262          DOI: 10.1107/S1399004715001030

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


  22 in total

1.  Structural changes in a cryo-cooled protein crystal owing to radiation damage.

Authors:  W P Burmeister
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-03

2.  Specific chemical and structural damage to proteins produced by synchrotron radiation.

Authors:  M Weik; R B Ravelli; G Kryger; S McSweeney; M L Raves; M Harel; P Gros; I Silman; J Kroon; J L Sussman
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-18       Impact factor: 11.205

3.  On the influence of the incident photon energy on the radiation damage in crystalline biological samples.

Authors:  Manfred S Weiss; Santosh Panjikar; Christoph Mueller-Dieckmann; Paul A Tucker
Journal:  J Synchrotron Radiat       Date:  2005-04-14       Impact factor: 2.616

4.  The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results.

Authors:  Gerd Rosenbaum; Randy W Alkire; Gwyndaf Evans; Frank J Rotella; Krzystof Lazarski; Rong Guang Zhang; Stephan L Ginell; Norma Duke; Istvan Naday; Jack Lazarz; Michael J Molitsky; Lisa Keefe; John Gonczy; Larry Rock; Ruslan Sanishvili; Martin A Walsh; Edwin Westbrook; Andrzej Joachimiak
Journal:  J Synchrotron Radiat       Date:  2005-12-22       Impact factor: 2.616

5.  Dose dependence of radiation damage for protein crystals studied at various X-ray energies.

Authors:  Nobutaka Shimizu; Kunio Hirata; Kazuya Hasegawa; Go Ueno; Masaki Yamamoto
Journal:  J Synchrotron Radiat       Date:  2006-12-15       Impact factor: 2.616

6.  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

7.  Energy dependence of site-specific radiation damage in protein crystals.

Authors:  Christina Homer; Laura Cooper; Ana Gonzalez
Journal:  J Synchrotron Radiat       Date:  2011-03-15       Impact factor: 2.616

Review 8.  Radiation damage in macromolecular cryocrystallography.

Authors:  Raimond B G Ravelli; Elspeth F Garman
Journal:  Curr Opin Struct Biol       Date:  2006-08-30       Impact factor: 6.809

9.  Slow cooling and temperature-controlled protein crystallography.

Authors:  Matthew Warkentin; Robert E Thorne
Journal:  J Struct Funct Genomics       Date:  2009-12-10

10.  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
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  11 in total

1.  Analysis of Global and Site-Specific Radiation Damage in Cryo-EM.

Authors:  Johan Hattne; Dan Shi; Calina Glynn; Chih-Te Zee; Marcus Gallagher-Jones; Michael W Martynowycz; Jose A Rodriguez; Tamir Gonen
Journal:  Structure       Date:  2018-04-26       Impact factor: 5.006

2.  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

3.  In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.

Authors:  Chia Ying Huang; Vincent Olieric; Pikyee Ma; Nicole Howe; Lutz Vogeley; Xiangyu Liu; Rangana Warshamanage; Tobias Weinert; Ezequiel Panepucci; Brian Kobilka; Kay Diederichs; Meitian Wang; Martin Caffrey
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-01-01       Impact factor: 7.652

4.  Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography.

Authors:  Kazuya Hasegawa; Keitaro Yamashita; Tomohiro Murai; Nipawan Nuemket; Kunio Hirata; Go Ueno; Hideo Ago; Toru Nakatsu; Takashi Kumasaka; Masaki Yamamoto
Journal:  J Synchrotron Radiat       Date:  2017-01-01       Impact factor: 2.616

5.  Lifetimes and spatio-temporal response of protein crystals in intense X-ray microbeams.

Authors:  Matthew A Warkentin; Hakan Atakisi; Jesse B Hopkins; Donald Walko; Robert E Thorne
Journal:  IUCrJ       Date:  2017-10-13       Impact factor: 4.769

6.  X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution.

Authors:  Markus Kubin; Jan Kern; Meiyuan Guo; Erik Källman; Rolf Mitzner; Vittal K Yachandra; Marcus Lundberg; Junko Yano; Philippe Wernet
Journal:  Phys Chem Chem Phys       Date:  2018-06-20       Impact factor: 3.676

7.  MicroED with the Falcon III direct electron detector.

Authors:  Johan Hattne; Michael W Martynowycz; Pawel A Penczek; Tamir Gonen
Journal:  IUCrJ       Date:  2019-08-17       Impact factor: 4.769

8.  Resolution and dose dependence of radiation damage in biomolecular systems.

Authors:  Hakan Atakisi; Lauren Conger; David W Moreau; Robert E Thorne
Journal:  IUCrJ       Date:  2019-09-18       Impact factor: 4.769

9.  RNA protects a nucleoprotein complex against radiation damage.

Authors:  Charles S Bury; John E McGeehan; Alfred A Antson; Ian Carmichael; Markus Gerstel; Mikhail B Shevtsov; Elspeth F Garman
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-04-26       Impact factor: 7.652

Review 10.  Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics.

Authors:  Ashutosh Srivastava; Tetsuro Nagai; Arpita Srivastava; Osamu Miyashita; Florence Tama
Journal:  Int J Mol Sci       Date:  2018-10-30       Impact factor: 5.923

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