Literature DB >> 25286840

Multi-crystal native SAD analysis at 6 keV.

Qun Liu1, Youzhong Guo1, Yanqi Chang1, Zheng Cai2, Zahra Assur3, Filippo Mancia3, Mark I Greene2, Wayne A Hendrickson1.   

Abstract

Anomalous diffraction signals from typical native macromolecules are very weak, frustrating their use in de novo structure determination. Here, native SAD procedures are described to enhance signal to noise in anomalous diffraction by using multiple crystals in combination with synchrotron X-rays at 6 keV. Increased anomalous signals were obtained at 6 keV compared with 7 keV X-ray energy, which was used for previous native SAD analyses. A feasibility test of multi-crystal-based native SAD phasing was performed at 3.2 Å resolution for a known tyrosine protein kinase domain, and real-life applications were made to two novel membrane proteins at about 3.0 Å resolution. The three applications collectively serve to validate the robust feasibility of native SAD phasing at lower energy.

Entities:  

Keywords:  anomalous diffraction; light-atom-only native SAD; phase determination; protein structure

Mesh:

Substances:

Year:  2014        PMID: 25286840      PMCID: PMC4188002          DOI: 10.1107/S1399004714013376

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


  37 in total

1.  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

2.  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

3.  Evolution of diffraction methods for solving crystal structures.

Authors:  Wayne A Hendrickson
Journal:  Acta Crystallogr A       Date:  2012-12-18       Impact factor: 2.290

4.  Challenges of sulfur SAD phasing as a routine method in macromolecular crystallography.

Authors:  James Doutch; Michael A Hough; S Samar Hasnain; Richard W Strange
Journal:  J Synchrotron Radiat       Date:  2011-11-29       Impact factor: 2.616

5.  Novel approach to phasing proteins: derivatization by short cryo-soaking with halides.

Authors:  Z Dauter; M Dauter; K R Rajashankar
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

6.  Experimental phasing with SHELXC/D/E: combining chain tracing with density modification.

Authors:  George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

7.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

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

9.  How good are my data and what is the resolution?

Authors:  Philip R Evans; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-06-13

10.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21
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  12 in total

1.  Progress in protein crystallography.

Authors:  Zbigniew Dauter; Alexander Wlodawer
Journal:  Protein Pept Lett       Date:  2016       Impact factor: 1.890

Review 2.  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

3.  Structural and Mechanistic Insights into the Latrophilin3-FLRT3 Complex that Mediates Glutamatergic Synapse Development.

Authors:  Fanomezana M Ranaivoson; Qun Liu; Francesca Martini; Francesco Bergami; Sventja von Daake; Sheng Li; David Lee; Borries Demeler; Wayne A Hendrickson; Davide Comoletti
Journal:  Structure       Date:  2015-07-30       Impact factor: 5.006

4.  A step towards long-wavelength protein crystallography: subjecting protein crystals to a vacuum.

Authors:  Santosh Panjikar; Lars Thomsen; Kane Michael O'Donnell; Alan Riboldi-Tunnicliffe
Journal:  J Appl Crystallogr       Date:  2015-05-09       Impact factor: 3.304

5.  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

6.  Data-collection strategy for challenging native SAD phasing.

Authors:  Vincent Olieric; Tobias Weinert; Aaron D Finke; Carolin Anders; Dianfan Li; Natacha Olieric; Camelia N Borca; Michel O Steinmetz; Martin Caffrey; Martin Jinek; Meitian Wang
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

7.  Structural mechanism of ligand activation in human calcium-sensing receptor.

Authors:  Yong Geng; Lidia Mosyak; Igor Kurinov; Hao Zuo; Emmanuel Sturchler; Tat Cheung Cheng; Prakash Subramanyam; Alice P Brown; Sarah C Brennan; Hee-Chang Mun; Martin Bush; Yan Chen; Trang X Nguyen; Baohua Cao; Donald D Chang; Matthias Quick; Arthur D Conigrave; Henry M Colecraft; Patricia McDonald; Qing R Fan
Journal:  Elife       Date:  2016-07-19       Impact factor: 8.140

8.  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

9.  Sample manipulation and data assembly for robust microcrystal synchrotron crystallography.

Authors:  Gongrui Guo; Martin R Fuchs; Wuxian Shi; John Skinner; Evanna Berman; Craig M Ogata; Wayne A Hendrickson; Sean McSweeney; Qun Liu
Journal:  IUCrJ       Date:  2018-04-19       Impact factor: 4.769

10.  A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software.

Authors:  Anastasia Mylona; Stephen Carr; Pierre Aller; Isabel Moraes; Richard Treisman; Gwyndaf Evans; James Foadi
Journal:  Crystals (Basel)       Date:  2017-08-04       Impact factor: 2.589

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