fragHAR: towards ab initio quantum crystallographic X-ray structure refinement for polypeptides and proteins

Justin Bergmann, Max Davidson, Esko Oksanen, Ulf Ryde, Dylan Jayatilaka

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Abstract

We describe the first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins, using a fragmentation approach to break up the protein into residues and solvent, and thereby speed up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations. We find that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR refinement on the complete unfragmented system when tested on di-, tri- and hexapeptides. The largest changes are for parameters describing hydrogen atoms involved in hydrogen-bond interactions, but we show that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speedups are observed for the larger systems. With this approach we are able to perform a highly parallelized HAR in reasonable times for large systems. The method is implemented in the TONTO software.
Original languageEnglish
Pages (from-to)158-165
Number of pages8
JournalIUCrJ
Volume7
Issue numberPart 2
DOIs
Publication statusPublished - 1 Mar 2020

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