Literature DB >> 21206061

Multi-crystal anomalous diffraction for low-resolution macromolecular phasing.

Qun Liu1, Zhen Zhang, Wayne A Hendrickson.   

Abstract

Multiwavelength anomalous diffraction (MAD) and single-wavelength anomalous diffraction (SAD) are the two most commonly used methods for de novo determination of macromolecular structures. Both methods rely on the accurate extraction of anomalous signals; however, because of factors such as poor intrinsic order, radiation damage, inadequate anomalous scatterers, poor diffraction quality and other noise-causing factors, the anomalous signal from a single crystal is not always good enough for structure solution. In this study, procedures for extracting more accurate anomalous signals by merging data from multiple crystals are devised and tested. SAD phasing tests were made with a relatively large (1456 ordered residues) poorly diffracting (d(min) = 3.5 Å) selenomethionyl protein (20 Se). It is quantified that the anomalous signal, success in substructure determination and accuracy of phases and electron-density maps all improve with an increase in the number of crystals used in merging. Structure solutions are possible when no single crystal can support structural analysis. It is proposed that such multi-crystal strategies may be broadly useful when only weak anomalous signals are available.

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Year:  2010        PMID: 21206061      PMCID: PMC3016016          DOI: 10.1107/S0907444910046573

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


  43 in total

1.  Single-wavelength anomalous diffraction phasing revisited.

Authors:  L M Rice; T N Earnest; A T Brunger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-11

2.  Anomalous signal of phosphorus used for phasing DNA oligomer: importance of data redundancy.

Authors:  Z Dauter; D A Adamiak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2001-06-21

3.  Substructure solution with SHELXD.

Authors:  Thomas R Schneider; George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-09-28

4.  Direct phasing of one-wavelength anomalous-scattering data.

Authors:  Q Hao
Journal:  J Synchrotron Radiat       Date:  2000-05-01       Impact factor: 2.616

5.  Anomalous signal indicators in protein crystallography.

Authors:  P H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-10-19

6.  Structure determination of VEGF-E by sulfur SAD.

Authors:  Armin Wagner; Michel Pieren; Clemens Schulze-Briese; Kurt Ballmer-Hofer; Andrea E Prota
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-10-18

7.  Integration, scaling, space-group assignment and post-refinement.

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

8.  Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure.

Authors:  W A Hendrickson; J R Horton; D M LeMaster
Journal:  EMBO J       Date:  1990-05       Impact factor: 11.598

Review 9.  Scaling and assessment of data quality.

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

10.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

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  39 in total

1.  In situ serial Laue diffraction on a microfluidic crystallization device.

Authors:  Sarah L Perry; Sudipto Guha; Ashtamurthy S Pawate; Robert Henning; Irina Kosheleva; Vukica Srajer; Paul J A Kenis; Zhong Ren
Journal:  J Appl Crystallogr       Date:  2014-11-18       Impact factor: 3.304

2.  Towards time-resolved serial crystallography in a microfluidic device.

Authors:  Ashtamurthy S Pawate; Vukica Šrajer; Jeremy Schieferstein; Sudipto Guha; Robert Henning; Irina Kosheleva; Marius Schmidt; Zhong Ren; Paul J A Kenis; Sarah L Perry
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-06-27       Impact factor: 1.056

3.  DNA-PKcs, Allostery, and DNA Double-Strand Break Repair: Defining the Structure and Setting the Stage.

Authors:  Dimitri Y Chirgadze; David B Ascher; Tom L Blundell; Bancinyane L Sibanda
Journal:  Methods Enzymol       Date:  2017-05-03       Impact factor: 1.600

4.  Graphene-based microfluidics for serial crystallography.

Authors:  Shuo Sui; Yuxi Wang; Kristopher W Kolewe; Vukica Srajer; Robert Henning; Jessica D Schiffman; Christos Dimitrakopoulos; Sarah L Perry
Journal:  Lab Chip       Date:  2016-08-02       Impact factor: 6.799

5.  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

6.  Multi-crystal native SAD analysis at 6 keV.

Authors:  Qun Liu; Youzhong Guo; Yanqi Chang; Zheng Cai; Zahra Assur; Filippo Mancia; Mark I Greene; Wayne A Hendrickson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-09-30

Review 7.  Anomalous diffraction in crystallographic phase evaluation.

Authors:  Wayne A Hendrickson
Journal:  Q Rev Biophys       Date:  2014-02       Impact factor: 5.318

Review 8.  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

9.  Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism.

Authors:  Michael C Thompson; Duilio Cascio; Todd O Yeates
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-04-24       Impact factor: 7.652

10.  A microfluidic approach for protein structure determination at room temperature via on-chip anomalous diffraction.

Authors:  Sarah L Perry; Sudipto Guha; Ashtamurthy S Pawate; Amrit Bhaskarla; Vinayak Agarwal; Satish K Nair; Paul J A Kenis
Journal:  Lab Chip       Date:  2013-07-05       Impact factor: 6.799

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