Literature DB >> 26432413

Crystallographic phasing from weak anomalous signals.

Qun Liu1, Wayne A Hendrickson2.   

Abstract

The exploitation of anomalous signals for biological structural solution is maturing. Single-wavelength anomalous diffraction (SAD) is dominant in de novo structure analysis. Nevertheless, for challenging structures where the resolution is low (dmin≥3.5Å) or where only lighter atoms (Z≤20) are present, as for native macromolecules, solved SAD structures are still scarce. With the recent rapid development in crystal handling, beamline instrumentation, optimization of data collection strategies, use of multiple crystals and structure determination technologies, the weak anomalous diffraction signals are now robustly measured and should be used for routine SAD structure determination. The review covers these recent advances on weak anomalous signals measurement, analysis and utilization.
Copyright © 2015 Elsevier Ltd. All rights reserved.

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Year:  2015        PMID: 26432413      PMCID: PMC4684729          DOI: 10.1016/j.sbi.2015.08.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  61 in total

1.  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

Review 2.  Micro-crystallography comes of age.

Authors:  Janet L Smith; Robert F Fischetti; Masaki Yamamoto
Journal:  Curr Opin Struct Biol       Date:  2012-09-26       Impact factor: 6.809

3.  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

4.  phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.

Authors:  Thomas C Terwilliger; Frank Dimaio; Randy J Read; David Baker; Gábor Bunkóczi; Paul D Adams; Ralf W Grosse-Kunstleve; Pavel V Afonine; Nathaniel Echols
Journal:  J Struct Funct Genomics       Date:  2012-03-15

5.  Towards automated crystallographic structure refinement with phenix.refine.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Nathaniel Echols; Jeffrey J Headd; Nigel W Moriarty; Marat Mustyakimov; Thomas C Terwilliger; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-03-16

6.  PRIGo: a new multi-axis goniometer for macromolecular crystallography.

Authors:  Sandro Waltersperger; Vincent Olieric; Claude Pradervand; Wayne Glettig; Marco Salathe; Martin R Fuchs; Adrian Curtin; Xiaoqiang Wang; Simon Ebner; Ezequiel Panepucci; Tobias Weinert; Clemens Schulze-Briese; Meitian Wang
Journal:  J Synchrotron Radiat       Date:  2015-05-09       Impact factor: 2.616

7.  Atomic-accuracy models from 4.5-Å cryo-electron microscopy data with density-guided iterative local refinement.

Authors:  Frank DiMaio; Yifan Song; Xueming Li; Matthias J Brunner; Chunfu Xu; Vincent Conticello; Edward Egelman; Thomas Marlovits; Yifan Cheng; David Baker
Journal:  Nat Methods       Date:  2015-02-23       Impact factor: 28.547

8.  Structure and substrate ion binding in the sodium/proton antiporter PaNhaP.

Authors:  David Wöhlert; Werner Kühlbrandt; Ozkan Yildiz
Journal:  Elife       Date:  2014-11-26       Impact factor: 8.140

9.  Crystal structure of the eukaryotic origin recognition complex.

Authors:  Franziska Bleichert; Michael R Botchan; James M Berger
Journal:  Nature       Date:  2015-03-11       Impact factor: 49.962

10.  Pushing the limits of sulfur SAD phasing: de novo structure solution of the N-terminal domain of the ectodomain of HCV E1.

Authors:  Kamel El Omari; Oleg Iourin; Jan Kadlec; Richard Fearn; David R Hall; Karl Harlos; Jonathan M Grimes; David I Stuart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-07-25
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  18 in total

Review 1.  Atomic-level analysis of membrane-protein structure.

Authors:  Wayne A Hendrickson
Journal:  Nat Struct Mol Biol       Date:  2016-06-07       Impact factor: 15.369

2.  The crystal structure of full-length Sizzled from Xenopus laevis yields insights into Wnt-antagonistic function of secreted Frizzled-related proteins.

Authors:  Qixin Bu; Zhiqiang Li; Junying Zhang; Fei Xu; Jianmei Liu; Heli Liu
Journal:  J Biol Chem       Date:  2017-08-14       Impact factor: 5.157

3.  Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.

Authors:  Takanori Nakane; Shinya Hanashima; Mamoru Suzuki; Haruka Saiki; Taichi Hayashi; Keisuke Kakinouchi; Shigeru Sugiyama; Satoshi Kawatake; Shigeru Matsuoka; Nobuaki Matsumori; Eriko Nango; Jun Kobayashi; Tatsuro Shimamura; Kanako Kimura; Chihiro Mori; Naoki Kunishima; Michihiro Sugahara; Yoko Takakyu; Shigeyuki Inoue; Tetsuya Masuda; Toshiaki Hosaka; Kensuke Tono; Yasumasa Joti; Takashi Kameshima; Takaki Hatsui; Makina Yabashi; Tsuyoshi Inoue; Osamu Nureki; So Iwata; Michio Murata; Eiichi Mizohata
Journal:  Proc Natl Acad Sci U S A       Date:  2016-10-31       Impact factor: 11.205

Review 4.  Serial femtosecond crystallography at the SACLA: breakthrough to dynamic structural biology.

Authors:  Eiichi Mizohata; Takanori Nakane; Yohta Fukuda; Eriko Nango; So Iwata
Journal:  Biophys Rev       Date:  2017-12-01

5.  Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ.

Authors:  Patrick J Salveson; Sepehr Haerianardakani; Alexander Thuy-Boun; Stan Yoo; Adam G Kreutzer; Borries Demeler; James S Nowick
Journal:  J Am Chem Soc       Date:  2018-09-06       Impact factor: 15.419

Review 6.  Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis.

Authors:  Qun Liu; Wayne A Hendrickson
Journal:  Methods Mol Biol       Date:  2017

7.  Protein structure determination by single-wavelength anomalous diffraction phasing of X-ray free-electron laser data.

Authors:  Karol Nass; Anton Meinhart; Thomas R M Barends; Lutz Foucar; Alexander Gorel; Andrew Aquila; Sabine Botha; R Bruce Doak; Jason Koglin; Mengning Liang; Robert L Shoeman; Garth Williams; Sebastien Boutet; Ilme Schlichting
Journal:  IUCrJ       Date:  2016-03-09       Impact factor: 4.769

8.  Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines.

Authors:  Daniele de Sanctis; Marcus Oscarsson; Alexander Popov; Olof Svensson; Gordon Leonard
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

9.  EIGER detector: application in macromolecular crystallography.

Authors:  Arnau Casanas; Rangana Warshamanage; Aaron D Finke; Ezequiel Panepucci; Vincent Olieric; Anne Nöll; Robert Tampé; Stefan Brandstetter; Andreas Förster; Marcus Mueller; Clemens Schulze-Briese; Oliver Bunk; Meitian Wang
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-08-31       Impact factor: 7.652

10.  Identification of the point of diminishing returns in high-multiplicity data collection for sulfur SAD phasing.

Authors:  Selina L S Storm; Fabio Dall'Antonia; Gleb Bourenkov; Thomas R Schneider
Journal:  J Synchrotron Radiat       Date:  2017-01-01       Impact factor: 2.616

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