Literature DB >> 18084073

Triclinic lysozyme at 0.65 A resolution.

Jiawei Wang1, Miroslawa Dauter, Randy Alkire, Andrzej Joachimiak, Zbigniew Dauter.   

Abstract

The crystal structure of triclinic hen egg-white lysozyme (HEWL) has been refined against diffraction data extending to 0.65 A resolution measured at 100 K using synchrotron radiation. Refinement with anisotropic displacement parameters and with the removal of stereochemical restraints for the well ordered parts of the structure converged with a conventional R factor of 8.39% and an R(free) of 9.52%. The use of full-matrix refinement provided an estimate of the variances in the derived parameters. In addition to the 129-residue protein, a total of 170 water molecules, nine nitrate ions, one acetate ion and three ethylene glycol molecules were located in the electron-density map. Eight sections of the main chain and many side chains were modeled with alternate conformations. The occupancies of the water sites were refined and this step is meaningful when assessed by use of the free R factor. A detailed description and comparison of the structure are made with reference to the previously reported triclinic HEWL structures refined at 0.925 A (at the low temperature of 120 K) and at 0.95 A resolution (at room temperature).

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Year:  2007        PMID: 18084073     DOI: 10.1107/S0907444907054224

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


  36 in total

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Journal:  Biophys J       Date:  2012-04-18       Impact factor: 4.033

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Journal:  FEBS J       Date:  2007-11-23       Impact factor: 5.542

5.  Protein flexibility: coordinate uncertainties and interpretation of structural differences.

Authors:  Alexander A Rashin; Abraham H L Rashin; Robert L Jernigan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-10-22

6.  A conformation-dependent stereochemical library improves crystallographic refinement even at atomic resolution.

Authors:  Dale E Tronrud; P Andrew Karplus
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-07-12

7.  The role of flexibility and molecular shape in the crystallization of proteins by surface mutagenesis.

Authors:  Yancho D Devedjiev
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-01-28       Impact factor: 1.056

8.  Systematic analysis of residual density suggests that a major limitation in well-refined X-ray structures of proteins is the omission of ordered solvent.

Authors:  Jimin Wang
Journal:  Protein Sci       Date:  2017-03-07       Impact factor: 6.725

9.  Polarizable atomic multipole X-ray refinement: application to peptide crystals.

Authors:  Michael J Schnieders; Timothy D Fenn; Vijay S Pande; Axel T Brunger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-08-14

10.  Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

Authors:  C Alejandro Velikovsky; Lu Deng; Satoshi Tasumi; Lakshminarayan M Iyer; Melissa C Kerzic; L Aravind; Zeev Pancer; Roy A Mariuzza
Journal:  Nat Struct Mol Biol       Date:  2009-06-21       Impact factor: 15.369

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