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Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus

Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular...

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Autores principales: Yoshimura, Masato, Chen, Nai-Chi, Guan, Hong-Hsiang, Chuankhayan, Phimonphan, Lin, Chien-Chih, Nakagawa, Atsushi, Chen, Chun-Jung
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932916/
https://www.ncbi.nlm.nih.gov/pubmed/27377380
http://dx.doi.org/10.1107/S2059798316007695
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author Yoshimura, Masato
Chen, Nai-Chi
Guan, Hong-Hsiang
Chuankhayan, Phimonphan
Lin, Chien-Chih
Nakagawa, Atsushi
Chen, Chun-Jung
author_facet Yoshimura, Masato
Chen, Nai-Chi
Guan, Hong-Hsiang
Chuankhayan, Phimonphan
Lin, Chien-Chih
Nakagawa, Atsushi
Chen, Chun-Jung
author_sort Yoshimura, Masato
collection PubMed
description Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures.
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spelling pubmed-49329162016-07-08 Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus Yoshimura, Masato Chen, Nai-Chi Guan, Hong-Hsiang Chuankhayan, Phimonphan Lin, Chien-Chih Nakagawa, Atsushi Chen, Chun-Jung Acta Crystallogr D Struct Biol Research Papers Molecular averaging, including noncrystallographic symmetry (NCS) averaging, is a powerful method for ab initio phase determination and phase improvement. Applications of the cross-crystal averaging (CCA) method have been shown to be effective for phase improvement after initial phasing by molecular replacement, isomorphous replacement, anomalous dispersion or combinations of these methods. Here, a two-step process for phase determination in the X-ray structural analysis of a new coat protein from a betanodavirus, Grouper nervous necrosis virus, is described in detail. The first step is ab initio structure determination of the T = 3 icosahedral virus-like particle using NCS averaging (NCSA). The second step involves structure determination of the protrusion domain of the viral molecule using cross-crystal averaging. In this method, molecular averaging and solvent flattening constrain the electron density in real space. To quantify these constraints, a new, simple and general indicator, free fraction (ff), is introduced, where ff is defined as the ratio of the volume of the electron density that is freely changed to the total volume of the crystal unit cell. This indicator is useful and effective to evaluate the strengths of both NCSA and CCA. Under the condition that a mask (envelope) covers the target molecule well, an ff value of less than 0.1, as a new rule of thumb, gives sufficient phasing power for the successful construction of new structures. International Union of Crystallography 2016-06-23 /pmc/articles/PMC4932916/ /pubmed/27377380 http://dx.doi.org/10.1107/S2059798316007695 Text en © Yoshimura et al. 2016 http://creativecommons.org/licenses/by/2.0/uk/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.
spellingShingle Research Papers
Yoshimura, Masato
Chen, Nai-Chi
Guan, Hong-Hsiang
Chuankhayan, Phimonphan
Lin, Chien-Chih
Nakagawa, Atsushi
Chen, Chun-Jung
Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title_full Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title_fullStr Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title_full_unstemmed Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title_short Ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
title_sort ab initio phasing by molecular averaging in real space with new criteria: application to structure determination of a betanodavirus
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932916/
https://www.ncbi.nlm.nih.gov/pubmed/27377380
http://dx.doi.org/10.1107/S2059798316007695
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