Real-space quantum-based refinement for cryo-EM: Q|R#3

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F68081707%3A_____%2F20%3A00540076" target="_blank" >RIV/68081707:_____/20:00540076 - isvavai.cz</a>

Result on the web

<a href="https://scripts.iucr.org/cgi-bin/paper?S2059798320013194" target="_blank" >https://scripts.iucr.org/cgi-bin/paper?S2059798320013194</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1107/S2059798320013194" target="_blank" >10.1107/S2059798320013194</a>

Result language

angličtina

Original language name

Real-space quantum-based refinement for cryo-EM: Q|R#3

Original language description

Electron cryo-microscopy (cryo-EM) is rapidly becoming a major competitor to X-ray crystallography, especially for large structures that are difficult or impossible to crystallize. While recent spectacular technological improvements have led to significantly higher resolution three-dimensional reconstructions, the average quality of cryo-EM maps is still at the low-resolution end of the range compared with crystallography. A long-standing challenge for atomic model refinement has been the production of stereochemically meaningful models for this resolution regime. Here, it is demonstrated that including accurate model geometry restraints derived from ab initio quantum-chemical calculations (HF-D3/6-31G) can improve the refinement of an example structure (chain A of PDB entry 3j63). The robustness of the procedure is tested for additional structures with up to 7000 atoms (PDB entry 3a5x and chain C of PDB entry 5fn5) using the less expensive semi-empirical (GFN1-xTB) model. The necessary algorithms enabling real-space quantum refinement have been implemented in the latest version of qr.refine and are described here.

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

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

—

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

12

Country of publishing house

GB - UNITED KINGDOM

Number of pages

8

Pages from-to

1184-1191

UT code for WoS article

000596508400004

EID of the result in the Scopus database

2-s2.0-85097036238