Literature DB >> 23633598

On optimal placement of molecules in the unit cell.

Zbigniew Dauter1.   

Abstract

There are currently no rules for a unified, standard way of placing macromolecular structures in the crystal lattice. An analysis of all possible symmetry-equivalent representations of molecular structures in various space groups leads to the concept of the anti-Cheshire symmetry and suggests that the center of a unique structural motif can always be placed within the selected asymmetric unit of the anti-Cheshire cell. The placement of structures according to this suggestion will ensure uniformity of presentation of all structurally equivalent Protein Data Bank models and will therefore diminish the possibility of confusing less crystallographically knowledgeable users of the PDB. The anti-Cheshire cells and their asymmetric units are defined and tabulated for all 65 space groups relevant to macromolecular crystallography that exhibit only rotational symmetry operations.

Keywords:  Cheshire symmetry; anti-Cheshire symmetry; placement of molecules

Mesh:

Year:  2013        PMID: 23633598      PMCID: PMC4005360          DOI: 10.1107/S0907444913002722

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


  3 in total

Review 1.  Racemic protein crystallography.

Authors:  Todd O Yeates; Stephen B H Kent
Journal:  Annu Rev Biophys       Date:  2012-03-14       Impact factor: 12.981

2.  Placement of molecules in (not out of) the cell.

Authors:  Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-12-20

3.  The interpretation of protein structures: total volume, group volume distributions and packing density.

Authors:  F M Richards
Journal:  J Mol Biol       Date:  1974-01-05       Impact factor: 5.469

  3 in total
  3 in total

1.  ACHESYM: an algorithm and server for standardized placement of macromolecular models in the unit cell.

Authors:  Marcin Kowiel; Mariusz Jaskolski; Zbigniew Dauter
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2014-11-28

2.  Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.

Authors:  Zbigniew Dauter; Alexander Wlodawer; Wladek Minor; Mariusz Jaskolski; Bernhard Rupp
Journal:  IUCrJ       Date:  2014-04-14       Impact factor: 4.769

3.  Covid-19.bioreproducibility.org: A web resource for SARS-CoV-2-related structural models.

Authors:  Dariusz Brzezinski; Marcin Kowiel; David R Cooper; Marcin Cymborowski; Marek Grabowski; Alexander Wlodawer; Zbigniew Dauter; Ivan G Shabalin; Miroslaw Gilski; Bernhard Rupp; Mariusz Jaskolski; Wladek Minor
Journal:  Protein Sci       Date:  2020-10-08       Impact factor: 6.993

  3 in total

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