Literature DB >> 11752767

On the use of low-resolution data for translation search in molecular replacement.

Andrei Fokine1, Alexandre Urzhumtsev.   

Abstract

Low-resolution reflections (approximately 15 A and lower) are very useful for the translation search in molecular replacement because they are less sensitive to model errors compared with the traditionally used reflections of resolution 4-10 A. At low resolution, however, the contribution from the bulk solvent is quite significant and corresponding structure factors calculated from a macromolecular model cannot be compared with experimental values if this contribution is neglected. The proposed method provides a way of fast translation searches where low-resolution reflections are taken into account. Test calculations using several experimental data sets show a dramatic improvement in the signal after the bulk-solvent correction and low-resolution reflections were included in the calculation; this improvement allowed unambiguous identification of the solution.

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Year:  2001        PMID: 11752767     DOI: 10.1107/s0108767301016476

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN: 0108-7673            Impact factor:   2.290


  5 in total

1.  A robust bulk-solvent correction and anisotropic scaling procedure.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-06-24

2.  Two conformational states in the crystal structure of the Homo sapiens cytoplasmic ribosomal decoding A site.

Authors:  Jiro Kondo; Alexandre Urzhumtsev; Eric Westhof
Journal:  Nucleic Acids Res       Date:  2006-02-01       Impact factor: 16.971

Review 3.  The solvent component of macromolecular crystals.

Authors:  Christian X Weichenberger; Pavel V Afonine; Katherine Kantardjieff; Bernhard Rupp
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-04-30

4.  Bulk-solvent and overall scaling revisited: faster calculations, improved results.

Authors:  P V Afonine; R W Grosse-Kunstleve; P D Adams; A Urzhumtsev
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-03-14

5.  The bacterial and mitochondrial ribosomal A-site molecular switches possess different conformational substates.

Authors:  Jiro Kondo; Eric Westhof
Journal:  Nucleic Acids Res       Date:  2008-03-16       Impact factor: 16.971

  5 in total

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