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Local and global analysis of macromolecular atomic displacement parameters.

ABSTRACT: 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.

SUBMITTER: Masmaliyeva RC

PROVIDER: S-EPMC7543658 | biostudies-literature | 2020 Oct

REPOSITORIES: biostudies-literature

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Local and global analysis of macromolecular atomic displacement parameters.

Masmaliyeva Rafiga C RC Babai Kave H KH Murshudov Garib N GN

Acta crystallographica. Section D, Structural biology 20200922 Pt 10

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 detect ...[more]

PMID: 33021494

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