Literature DB >> 19770506

On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.

Santosh Panjikar1, Venkataraman Parthasarathy, Victor S Lamzin, Manfred S Weiss, Paul A Tucker.   

Abstract

A combination of molecular replacement and single-wavelength anomalous diffraction phasing has been incorporated into the automated structure-determination platform Auto-Rickshaw. The complete MRSAD procedure includes molecular replacement, model refinement, experimental phasing, phase improvement and automated model building. The improvement over the standard SAD or MR approaches is illustrated by ten test cases taken from the JCSG diffraction data-set database. Poor MR or SAD phases with phase errors larger than 70 degrees can be improved using the described procedure and a large fraction of the model can be determined in a purely automatic manner from X-ray data extending to better than 2.6 A resolution.

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Year:  2009        PMID: 19770506      PMCID: PMC2756167          DOI: 10.1107/S0907444909029643

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


  43 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.  A stochastic approach to molecular replacement.

Authors:  N M Glykos; M Kokkinidis
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-02

3.  Rapid automated molecular replacement by evolutionary search.

Authors:  C R Kissinger; D K Gehlhaar; D B Fogel
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-02

4.  General quadratic functions in real and reciprocal space and their application to likelihood phasing.

Authors:  K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-12

5.  Pushing the boundaries of molecular replacement with maximum likelihood.

Authors:  R J Read
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2001-09-21

6.  Evolutionary transition pathways for changing peptide ligand specificity and structure.

Authors:  U Hoffmüller; T Knaute; M Hahn; W Höhne; J Schneider-Mergener; A Kramer
Journal:  EMBO J       Date:  2000-09-15       Impact factor: 11.598

7.  Automated protein model building combined with iterative structure refinement.

Authors:  A Perrakis; R Morris; V S Lamzin
Journal:  Nat Struct Biol       Date:  1999-05

Review 8.  Automation of the collection and processing of X-ray diffraction data -- a generic approach.

Authors:  A G W Leslie; H R Powell; G Winter; O Svensson; D Spruce; S McSweeney; D Love; S Kinder; E Duke; C Nave
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

9.  Reciprocal-space solvent flattening.

Authors:  T C Terwilliger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-11

10.  Maximum-likelihood density modification.

Authors:  T C Terwilliger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2000-08
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  76 in total

1.  Crystal structure of the Lassa virus nucleoprotein-RNA complex reveals a gating mechanism for RNA binding.

Authors:  Kathryn M Hastie; Tong Liu; Sheng Li; Liam B King; Nhi Ngo; Michelle A Zandonatti; Virgil L Woods; Juan Carlos de la Torre; Erica Ollmann Saphire
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-14       Impact factor: 11.205

2.  Fast high-pressure freezing of protein crystals in their mother liquor.

Authors:  Anja Burkhardt; Martin Warmer; Saravanan Panneerselvam; Armin Wagner; Athina Zouni; Carina Glöckner; Rudolph Reimer; Heinrich Hohenberg; Alke Meents
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-03-31

3.  The terminal phycobilisome emitter, LCM: A light-harvesting pigment with a phytochrome chromophore.

Authors:  Kun Tang; Wen-Long Ding; Astrid Höppner; Cheng Zhao; Lun Zhang; Yusaku Hontani; John T M Kennis; Wolfgang Gärtner; Hugo Scheer; Ming Zhou; Kai-Hong Zhao
Journal:  Proc Natl Acad Sci U S A       Date:  2015-12-15       Impact factor: 11.205

4.  Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.

Authors:  Kathryn M Hastie; Michelle Zandonatti; Tong Liu; Sheng Li; Virgil L Woods; Erica Ollmann Saphire
Journal:  J Virol       Date:  2016-04-14       Impact factor: 5.103

5.  Structural basis for RNA recognition in roquin-mediated post-transcriptional gene regulation.

Authors:  Andreas Schlundt; Gitta A Heinz; Robert Janowski; Arie Geerlof; Ralf Stehle; Vigo Heissmeyer; Dierk Niessing; Michael Sattler
Journal:  Nat Struct Mol Biol       Date:  2014-07-13       Impact factor: 15.369

6.  Crystal structure of subunits D and F in complex gives insight into energy transmission of the eukaryotic V-ATPase from Saccharomyces cerevisiae.

Authors:  Asha Manikkoth Balakrishna; Sandip Basak; Malathy Sony Subramanian Manimekalai; Gerhard Grüber
Journal:  J Biol Chem       Date:  2014-12-12       Impact factor: 5.157

7.  The structure of Arabidopsis thaliana OST1 provides insights into the kinase regulation mechanism in response to osmotic stress.

Authors:  Cristina Yunta; Martín Martínez-Ripoll; Jian-Kang Zhu; Armando Albert
Journal:  J Mol Biol       Date:  2011-10-01       Impact factor: 5.469

8.  Structural insights into the mechanisms of Mg2+ uptake, transport, and gating by CorA.

Authors:  Albert Guskov; Nurhuda Nordin; Aline Reynaud; Henrik Engman; Anna-Karin Lundbäck; Agnes Jin Oi Jong; Tobias Cornvik; Terri Phua; Said Eshaghi
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-22       Impact factor: 11.205

9.  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

10.  The magic triangle goes MAD: experimental phasing with a bromine derivative.

Authors:  Tobias Beck; Tim Gruene; George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24
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