Literature DB >> 25532136

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

Gábor Bunkóczi1, Airlie J McCoy1, Nathaniel Echols2, Ralf W Grosse-Kunstleve2, Paul D Adams2, James M Holton3, Randy J Read1, Thomas C Terwilliger4.   

Abstract

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases.

Entities:  

Mesh:

Substances:

Year:  2014        PMID: 25532136      PMCID: PMC4312553          DOI: 10.1038/nmeth.3212

Source DB:  PubMed          Journal:  Nat Methods        ISSN: 1548-7091            Impact factor:   28.547


  40 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Substructure solution with SHELXD.

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

3.  wARP: improvement and extension of crystallographic phases by weighted averaging of multiple-refined dummy atomic models.

Authors:  A Perrakis; T K Sixma; K S Wilson; V S Lamzin
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-07-01

4.  Crystal structure of MtnX phosphatase from Bacillus subtilis at 2.0 angstroms resolution provides a structural basis for bipartite phosphomonoester hydrolysis of 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate.

Authors:  Qingping Xu; Kumar Singh Saikatendu; S Sri Krishna; Daniel McMullan; Polat Abdubek; Sanjay Agarwalla; Eileen Ambing; Tamara Astakhova; Herbert L Axelrod; Dennis Carlton; Hsiu-Ju Chiu; Thomas Clayton; Michael DiDonato; Lian Duan; Marc-André Elsliger; Julie Feuerhelm; Slawomir K Grzechnik; Joanna Hale; Eric Hampton; Gye Won Han; Justin Haugen; Lukasz Jaroszewski; Kevin K Jin; Heath E Klock; Mark W Knuth; Eric Koesema; Mitchell D Miller; Andrew T Morse; Edward Nigoghossian; Linda Okach; Silvya Oommachen; Jessica Paulsen; Ron Reyes; Christopher L Rife; Robert Schwarzenbacher; Henry van den Bedem; Aprilfawn White; Guenter Wolf; Keith O Hodgson; John Wooley; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson
Journal:  Proteins       Date:  2007-11-01

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

Authors:  Michele Cianci; John R Helliwell; Atsuo Suzuki
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-11-18

6.  Automated MAD and MIR structure solution.

Authors:  T C Terwilliger; J Berendzen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-04

7.  Experimental phasing: best practice and pitfalls.

Authors:  Airlie J McCoy; Randy J Read
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

8.  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

9.  Deduced RNA binding mechanism of ThiI based on structural and binding analyses of a minimal RNA ligand.

Authors:  Yoshikazu Tanaka; Shiori Yamagata; Yu Kitago; Yoko Yamada; Sarin Chimnaronk; Min Yao; Isao Tanaka
Journal:  RNA       Date:  2009-06-09       Impact factor: 4.942

10.  Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Authors:  Thomas C Terwilliger; Ralf W Grosse-Kunstleve; Pavel V Afonine; Nigel W Moriarty; Peter H Zwart; Li Wei Hung; Randy J Read; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05
View more
  12 in total

Review 1.  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

Review 2.  Contemporary Use of Anomalous Diffraction in Biomolecular Structure Analysis.

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

3.  Initiating heavy-atom-based phasing by multi-dimensional molecular replacement.

Authors:  Bjørn Panyella Pedersen; Pontus Gourdon; Xiangyu Liu; Jesper Lykkegaard Karlsen; Poul Nissen
Journal:  Acta Crystallogr D Struct Biol       Date:  2016-03-01       Impact factor: 7.652

4.  Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm.

Authors:  Hongxing He; Hengrui Fang; Mitchell D Miller; George N Phillips; Wu Pei Su
Journal:  Acta Crystallogr A Found Adv       Date:  2016-07-15       Impact factor: 2.290

5.  Selenium single-wavelength anomalous diffraction de novo phasing using an X-ray-free electron laser.

Authors:  Mark S Hunter; Chun Hong Yoon; Hasan DeMirci; Raymond G Sierra; E Han Dao; Radman Ahmadi; Fulya Aksit; Andrew L Aquila; Halilibrahim Ciftci; Serge Guillet; Matt J Hayes; Thomas J Lane; Meng Liang; Ulf Lundström; Jason E Koglin; Paul Mgbam; Yashas Rao; Lindsey Zhang; Soichi Wakatsuki; James M Holton; Sébastien Boutet
Journal:  Nat Commun       Date:  2016-11-04       Impact factor: 14.919

6.  Maximum-likelihood determination of anomalous substructures.

Authors:  Randy J Read; Airlie J McCoy
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-02-01       Impact factor: 7.652

7.  An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features.

Authors:  Isabel Usón; George M Sheldrick
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-02-01       Impact factor: 7.652

8.  Synchrotron microcrystal native-SAD phasing at a low energy.

Authors:  Gongrui Guo; Ping Zhu; Martin R Fuchs; Wuxian Shi; Babak Andi; Yuan Gao; Wayne A Hendrickson; Sean McSweeney; Qun Liu
Journal:  IUCrJ       Date:  2019-05-03       Impact factor: 4.769

9.  Likelihood-based estimation of substructure content from single-wavelength anomalous diffraction (SAD) intensity data.

Authors:  Kaushik S Hatti; Airlie J McCoy; Randy J Read
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-06-18       Impact factor: 7.652

10.  Evaluating crystallographic likelihood functions using numerical quadratures.

Authors:  Petrus H Zwart; Elliott D Perryman
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-07-27       Impact factor: 7.652

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.