Local and global analysis of macromolecular Atomic Displacement Parameters

Abstract

This paper describes the global and local analyses of Atomic Displacement Parameters (ADP) of macromolecules solved and refined using X-ray crystallography method. It is shown that the distribution of ADPs follows the (mixture of) Shifted Inverse Gamma distribution(s). The parameters of the mixture of SIGDs are estimated using Expectation/Maximisation methods. In addition, a method for resolution and individual ADP dependent local analysis of neighbouring atoms has been designed. This method facilitates the detection of the mismodelled atoms and indicates potential identity of heavy metal atoms. It also helps in detecting of disordered and/or wrongly modelled ligands. Both global and local analyses can be used to detect errors in atomic structures thus helping in (re)building, refinement and validation of macromolecular structures. It can also serve as an additional validation tool during data deposition to the PDB. SynopsisMacromolecular atomic B value distributions have been modelled using a mixture of Shifted Inverse Gamma Distribution. Also, B value and resolution dependent local ADP differences have been applied for validation of heavy atoms and ligands.