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Local and global analysis of macromolecular atomic displacement parameters
Author(s) -
Masmaliyeva Rafiga C.,
Babai Kave H.,
Murshudov Garib N.
Publication year - 2020
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.374
H-Index - 138
ISSN - 2059-7983
DOI - 10.1107/s2059798320011043
Subject(s) - macromolecule , displacement (psychology) , inverse , maximization , distribution (mathematics) , expectation–maximization algorithm , resolution (logic) , biological system , statistical physics , algorithm , chemistry , computer science , computational physics , crystallography , physics , mathematics , mathematical optimization , statistics , maximum likelihood , geometry , biology , artificial intelligence , mathematical analysis , psychology , biochemistry , psychotherapist
This paper describes the global and local analysis of atomic displacement parameters (ADPs) of macromolecules in X‐ray crystallography. The distribution of ADPs is shown to follow the shifted inverse‐gamma distribution or a mixture of these distributions. The mixture parameters are estimated using the expectation–maximization algorithm. In addition, a method for the resolution‐ and individual ADP‐dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of mismodelled atoms, heavy‐metal atoms and disordered and/or incorrectly modelled ligands. Both global and local analyses can be used to detect errors in atomic models, thus helping in the (re)building, refinement and validation of macromolecular structures. This method can also serve as an additional validation tool during PDB deposition.