Including crystallographic symmetry in quantum‐based refinement: Q|R#2. Issue 1 (2nd January 2020)

• Record Type: Journal Article
• Authors: Zheng, Min; Biczysko, Malgorzata; Xu, Yanting; Moriarty, Nigel W.; Kruse, Holger; Urzhumtsev, Alexandre; Waller, Mark P.; Afonine, Pavel V.
• Is Part Of: Acta crystallographica. Volume 76:Issue 1(2020)
• Page Start: 41
• Page End: 50
• Publication Date: 2020-01-02
• Subjects: quantum refinement -- symmetry -- fragmentation -- graph‐based clustering -- crystallography -- cryo‐EM -- Hartree–Fock theory; X-ray crystallography -- Periodicals; Crystallography -- Periodicals; Molecular biology -- Periodicals; Molecular structure -- Periodicals; Biomolecules -- Structure -- Periodicals; Cytology -- Periodicals; Biomolecules -- Structure; Crystallography; Cytology; Molecular biology; Molecular structure; X-ray crystallography; Periodicals; 548
• DOI: 10.1107/S2059798319015122
• Languages: English
• ISSNs: 2059-7983

Abstract

Abstract : The C‐terminal coiled‐coil domain of transient receptor potential channel TRPP3 in space group P 321 (PDB entry 4gif ) is re‐refined with restraints from quantum chemistry using Hartree–Fock theory. Abstract : Three‐dimensional structure models refined using low‐resolution data from crystallographic or electron cryo‐microscopy experiments can benefit from high‐quality restraints derived from quantum‐chemical methods. However, nonperiodic atom‐centered quantum‐chemistry codes do not inherently account for nearest‐neighbor interactions of crystallographic symmetry‐related copies in a satisfactory way. Here, these nearest‐neighbor effects have been included in the model by expanding to a super‐cell and then truncating the super‐cell to only include residues from neighboring cells that are interacting with the asymmetric unit. In this way, the fragmentation approach can adequately and efficiently include nearest‐neighbor effects. It has previously been shown that a moderately sized X‐ray structure can be treated using quantum methods if a fragmentation approach is applied. In this study, a target protein (PDB entry 4gif ) was partitioned into a number of large fragments. The use of large fragments (typically hundreds of atoms) is tractable when a GPU‐based package such as TeraChem is employed or cheaper (semi‐empirical) methods are used. The QM calculations were run at the HF‐D3/6‐31G level. The models refined using a recently developed semi‐empirical method (GFN2‐xTB) were compared and contrasted. To validate the refinement procedure for a non‐ P 1 structure, a standard set of crystallographic metrics were used. The robustness of the implementation is shown by refining 13 additional protein models across multiple space groups and a summary of the refinement metrics is presented.