Literature DB >> 16369097

Intensity statistics in twinned crystals with examples from the PDB.

Andrey A Lebedev1, Alexei A Vagin, Garib N Murshudov.   

Abstract

Entries deposited in the Protein Data Bank as of February 2004 for which both model and X-ray data were available were analysed to identify cases of twinning using such simple statistics as the R factor between potential twin-related reflections. Careful consideration of all identified twins showed that in many cases twinning was ignored during structure solution and refinement. Manual analysis of the models showed that twinning often occurs in association with rotational pseudosymmetry parallel to the twinning operator. The coexistence of these two phenomena complicates the detection and diagnostics of twinning using currently available twinning tests. It was concluded that a twinning-detection step should be incorporated in every stage of structure analysis from data acquisition to refinement and validation.

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Year:  2005        PMID: 16369097     DOI: 10.1107/S0907444905036759

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


  37 in total

1.  Crystallographic study of a MATE transporter presents a difficult case in structure determination with low-resolution, anisotropic data and crystal twinning.

Authors:  Jindrich Symersky; Yi Guo; Jimin Wang; Min Lu
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-10-31

2.  Rotational order-disorder structure of fluorescent protein FP480.

Authors:  Sergei Pletnev; Kateryna S Morozova; Vladislav V Verkhusha; Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-08-06

Review 3.  Determination of protein structures--a series of fortunate events.

Authors:  Maksymilian Chruszcz; Alexander Wlodawer; Wladek Minor
Journal:  Biophys J       Date:  2008-04-25       Impact factor: 4.033

4.  Elucidation of the specific function of the conserved threonine triad responsible for human L-asparaginase autocleavage and substrate hydrolysis.

Authors:  Julian Nomme; Ying Su; Arnon Lavie
Journal:  J Mol Biol       Date:  2014-04-22       Impact factor: 5.469

5.  BraggNet: integrating Bragg peaks using neural networks.

Authors:  Brendan Sullivan; Rick Archibald; Jahaun Azadmanesh; Venu Gopal Vandavasi; Patricia S Langan; Leighton Coates; Vickie Lynch; Paul Langan
Journal:  J Appl Crystallogr       Date:  2019-07-26       Impact factor: 3.304

6.  Expression, purification and crystallization of the ecto-enzymatic domain of rat E-NTPDase1 CD39.

Authors:  Xiaotian Zhong; Madhavan Buddha; Guido Guidotti; Ron Kriz; Will Somers; Lidia Mosyak
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2008-10-31

7.  Detection and correction of underassigned rotational symmetry prior to structure deposition.

Authors:  Billy K Poon; Ralf W Grosse-Kunstleve; Peter H Zwart; Nicholas K Sauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-04-21

8.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

9.  phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Vincent B Chen; Jeffrey J Headd; Nigel W Moriarty; Jane S Richardson; David C Richardson; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  J Appl Crystallogr       Date:  2010-05-22       Impact factor: 3.304

10.  Engineered variants of InlB with an additional leucine-rich repeat discriminate between physiologically relevant and packing contacts in crystal structures of the InlB:MET complex.

Authors:  Hartmut H Niemann; Ermanno Gherardi; Willem M Bleymüller; Dirk W Heinz
Journal:  Protein Sci       Date:  2012-09-17       Impact factor: 6.725

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