Literature DB >> 19018096

The interdependence of wavelength, redundancy and dose in sulfur SAD experiments.

Michele Cianci1, John R Helliwell, Atsuo Suzuki.   

Abstract

In the last decade, the popularity of sulfur SAD anomalous dispersion experiments has spread rapidly among synchrotron users as a quick and streamlined way of solving the phase problem in macromolecular crystallography. On beamline 10 at SRS (Daresbury Laboratory, UK), a versatile design has allowed test data sets to be collected at six wavelengths between 0.979 and 2.290 A in order to evaluate the importance and the interdependence of experimental variables such as the Bijvoet ratio, wavelength, resolution limit, data redundancy and absorbed X-ray dose in the sample per data set. All the samples used in the experiments were high-quality hen egg-white lysozyme crystals. X-radiation damage was found to affect disulfide bridges after the crystals had been given a total dose of 0.20 x 10(7) Gy. However, with such a total dose, it was still possible in all cases to find a strategy to collect data sets to determine the sulfur substructure and produce good-quality phases by choosing an optimum combination of wavelength, exposure time and redundancy. A |Delta(ano)|/sigma(Delta(ano)) greater than 1.5 for all resolution shells was a necessary requirement for successful sulfur SAD substructure location. Provided this is achieved, it seems possible to find an optimum compromise between wavelength, redundancy and dose to provide phasing information. The choice of the wavelength should then follow the sample composition and the diffracting properties of the crystal. For strongly diffracting crystals, wavelengths equal or shorter than 1.540 A can be selected to capture the available data (provided the Bijvoet ratio is reasonable), while a longer wavelength, to gain as high a Bijvoet ratio as possible, must be used for more weakly diffracting crystals. These results suggest that an approach to a sulfur SAD experiment based on a complete description of the crystal system and the instrument for data collection is useful.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 19018096     DOI: 10.1107/S0907444908030503

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


  22 in total

1.  Bioconjugate of lysozyme and the antibacterial marine sesquiterpene quinone avarone and its derivatives.

Authors:  Irena Novaković; Uroš Anđelković; Mario Zlatović; Miroslav J Gašić; Dušan Sladić
Journal:  Bioconjug Chem       Date:  2012-01-04       Impact factor: 4.774

2.  Can radiation damage to protein crystals be reduced using small-molecule compounds?

Authors:  Jan Kmetko; Matthew Warkentin; Ulrich Englich; Robert E Thorne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-09-08

3.  Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

Authors:  Gábor Bunkóczi; Airlie J McCoy; Nathaniel Echols; Ralf W Grosse-Kunstleve; Paul D Adams; James M Holton; Randy J Read; Thomas C Terwilliger
Journal:  Nat Methods       Date:  2014-12-22       Impact factor: 28.547

4.  Structures from anomalous diffraction of native biological macromolecules.

Authors:  Qun Liu; Tassadite Dahmane; Zhen Zhang; Zahra Assur; Julia Brasch; Lawrence Shapiro; Filippo Mancia; Wayne A Hendrickson
Journal:  Science       Date:  2012-05-25       Impact factor: 47.728

5.  Room-temperature X-ray diffraction studies of cisplatin and carboplatin binding to His15 of HEWL after prolonged chemical exposure.

Authors:  Simon W M Tanley; Antoine M M Schreurs; Loes M J Kroon-Batenburg; John R Helliwell
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-10-26

6.  S-SAD phasing study of death receptor 6 and its solution conformation revealed by SAXS.

Authors:  Heng Ru; Lixia Zhao; Wei Ding; Lianying Jiao; Neil Shaw; Wenguang Liang; Liguo Zhang; Li-Wei Hung; Naohiro Matsugaki; Soichi Wakatsuki; Zhi-Jie Liu
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-04-17

7.  Noncovalent polymerization of mesogens crystallizes lysozyme: correlation between nonamphiphilic lyotropic liquid crystal phase and protein crystal formation.

Authors:  Karen A Simon; Gauri S Shetye; Ulrich Englich; Lei Wu; Yan-Yeung Luk
Journal:  Langmuir       Date:  2011-08-04       Impact factor: 3.882

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.  Parallel Evolution of Chemokine Binding by Structurally Related Herpesvirus Decoy Receptors.

Authors:  Olga Y Lubman; Daved H Fremont
Journal:  Structure       Date:  2015-12-03       Impact factor: 5.006

10.  Structure of the Archaeoglobus fulgidus orphan ORF AF1382 determined by sulfur SAD from a moderately diffracting crystal.

Authors:  Jin-Yi Zhu; Zheng-Qing Fu; Lirong Chen; Hao Xu; John Chrzas; John Rose; Bi-Cheng Wang
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-08-18
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.