Cryo-EM single-particle structure refinement and map calculation using Servalcat.
Acta Crystallogr D Struct Biol
; 77(Pt 10): 1282-1291, 2021 Oct 01.
Article
em En
| MEDLINE
| ID: mdl-34605431
ABSTRACT
In 2020, cryo-EM single-particle analysis achieved true atomic resolution thanks to technological developments in hardware and software. The number of high-resolution reconstructions continues to grow, increasing the importance of the accurate determination of atomic coordinates. Here, a new Python package and program called Servalcat is presented that is designed to facilitate atomic model refinement. Servalcat implements a refinement pipeline using the program REFMAC5 from the CCP4 package. After the refinement, Servalcat calculates a weighted Fo - Fc difference map, which is derived from Bayesian statistics. This map helps manual and automatic model building in real space, as is common practice in crystallography. The Fo - Fc map helps in the visualization of weak features including hydrogen densities. Although hydrogen densities are weak, they are stronger than in the electron-density maps produced by X-ray crystallography, and some H atoms are even visible at â¼1.8â
Å resolution. Servalcat also facilitates atomic model refinement under symmetry constraints. If point-group symmetry has been applied to the map during reconstruction, the asymmetric unit model is refined with the appropriate symmetry constraints.
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1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Algoritmos
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Software
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Microscopia Crioeletrônica
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Substâncias Macromoleculares
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Imagem Individual de Molécula
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Hidrogênio
Tipo de estudo:
Guideline
Idioma:
En
Ano de publicação:
2021
Tipo de documento:
Article