Including crystallographic symmetry in quantum-based refinement: Q|R#2

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F20%3A00524319" target="_blank" >RIV/68081707:_____/20:00524319 - isvavai.cz</a>

Result on the web

<a href="http://scripts.iucr.org/cgi-bin/paper?S2059798319015122" target="_blank" >http://scripts.iucr.org/cgi-bin/paper?S2059798319015122</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1107/S2059798319015122" target="_blank" >10.1107/S2059798319015122</a>

Result language

angličtina

Original language name

Including crystallographic symmetry in quantum-based refinement: Q|R#2

Original language description

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-P1 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.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10608 - Biochemistry and molecular biology

Project

<a href="/en/project/EF15_003%2F0000477" target="_blank" >EF15_003/0000477: Structural gymnastics of nucleic acids: from molecular principles through biological functions to therapeutic targets.</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Acta Crystallographica Section D-Structural Biology

ISSN

2059-7983

e-ISSN

—

Volume of the periodical

76

Issue of the periodical within the volume

JAN 1 2020

Country of publishing house

GB - UNITED KINGDOM

Number of pages

10

Pages from-to

41-50

UT code for WoS article

000505517700005

EID of the result in the Scopus database

2-s2.0-85077626339