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Transferable aspherical atom model refinement of protein and DNA structures against ultrahigh‐resolution X‐ray data
Author(s) -
Malinska Maura,
Dauter Zbigniew
Publication year - 2016
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/s2059798316006355
Subject(s) - crystallography , random hexamer , chemistry , atom (system on chip) , electron density , charge density , molecular physics , molecule , resolution (logic) , bond length , lone pair , atomic physics , electron , physics , crystal structure , organic chemistry , quantum mechanics , artificial intelligence , computer science , embedded system
In contrast to the independent‐atom model (IAM), in which all atoms are assumed to be spherical and neutral, the transferable aspherical atom model (TAAM) takes into account the deformed valence charge density resulting from chemical bond formation and the presence of lone electron pairs. Both models can be used to refine small and large molecules, e.g. proteins and nucleic acids, against ultrahigh‐resolution X‐ray diffraction data. The University at Buffalo theoretical databank of aspherical pseudo‐atoms has been used in the refinement of an oligopeptide, of Z‐DNA hexamer and dodecamer duplexes, and of bovine trypsin. The application of the TAAM to these data improves the quality of the electron‐density maps and the visibility of H atoms. It also lowers the conventional R factors and improves the atomic displacement parameters and the results of the Hirshfeld rigid‐bond test. An additional advantage is that the transferred charge density allows the estimation of Coulombic interaction energy and electrostatic potential.