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

Date Published: July 01, 2016

Publisher: International Union of Crystallography

Author(s): Masato Yoshimura, Nai-Chi Chen, Hong-Hsiang Guan, Phimonphan Chuankhayan, Chien-Chih Lin, Atsushi Nakagawa, Chun-Jung Chen.


A two-step process of phase determination in the X-ray structural analysis of the coat protein of a betanodavirus is described. A new indicator, the free fraction, for molecular averaging in real space is introduced to effectively evaluate the phasing power in order to enhance the success of determining new structures.

Partial Text

The molecular averaging method in real space, including noncrystallographic symmetry (NCS) averaging and cross-crystal averaging (CCA), coupled with solvent flattening, has proved to be powerful in improving the determination of the phases in protein crystallography. As a case in point, NCS averaging (NCSA) with phase extension of icosahedral viruses is a common procedure for phase improvement after initial calculations based on molecular replacement (MR) using a density map from a cryo-electron microscope, a similar model or initial experimental phases from isomorphous replacement or anomalous dispersion. Since the successful structure determination of the human common cold virus serotype 14 (Rossmann et al., 1985 ▸; Arnold et al., 1987 ▸), several virus structures have been solved using NCSA with phase extension. As the phasing power of NCSA is effective, the possibility of ab initio phase determination has been proposed. The feasibility of ab initio phase determination has been demonstrated for spherical viruses (Tsao et al., 1992 ▸). Ab initio trials and procedures have been reported for known icosahedral viruses (Taka et al., 2005 ▸). An assessment of the application of NCSA to icosahedral viruses, together with a detailed investigation of successful and unsuccessful cases, has also appeared (Plevka et al., 2011 ▸).




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