Abstract
Hemihedral twinning is a crystal-growth anomaly in which a specimen is composed of two crystal domains that coincide with each other in three dimensions. However, the orientations of the crystal lattices in the two domains differ in a specific way. In diffraction data collected from hemihedrally twinned crystals, each observed intensity contains contributions from both of the domains. With perfect hemihedral twinning, the two domains have the same volumes and the observed intensities do not contain sufficient information to detwin the data. Here, the use of molecular replacement and of noncrystallographic symmetry (NCS) averaging to detwin a 2.1 Å resolution data set for Aichi virus 1 affected by perfect hemihedral twinning is described. The NCS averaging enabled the correction of errors in the detwinning introduced by the differences between the molecular-replacement model and the crystallized structure. The procedure permitted the structure to be determined from a molecular-replacement model that had 16% sequence identity and a 1.6 Å r.m.s.d. for C(α) atoms in comparison to the crystallized structure. The same approach could be used to solve other data sets affected by perfect hemihedral twinning from crystals with NCS.
Highlights
Aichi virus 1 (AiV1) is a member of the Kobuvirus genus belonging to the Picornaviridae family of small non-enveloped viruses (Yamashita et al, 1991)
This paper focuses on the utilization of noncrystallographic symmetry (NCS) averaging to solve a structure from a data set affected by perfect hemihedral twinning
Green monkey kidney (GMK) cells were grown on 150 mm diameter plates to 70% confluency in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% foetal bovine serum (FBS; Sigma–Aldrich). 60 plates of green monkey kidney cells were infected with AiV1 with a multiplicity of infection (MOI) of 0.1
Summary
Aichi virus 1 (AiV1) is a member of the Kobuvirus genus belonging to the Picornaviridae family of small non-enveloped viruses (Yamashita et al, 1991). The two domains are related by the twinning operator, but not by their crystallographic symmetry (Yeates, 1997; Parsons, 2003). Partial hemihedral twinning does not obscure the true crystallographic symmetry because the pairs of reflections related by the twinning operator have different intensities (Parsons, 2003). The true crystallographic intensities can be calculated, using the value, based on (3) and (4) (Grainger, 1969; Yeates, 1997): Iðh1Þ 1⁄4 1⁄2ð1 À ÞIobsðh1Þ À Iobsðh2Þ=ð1 À 2 Þ; ð3Þ. We report the structure determination of an AiV1 virion based on diffraction data affected by perfect hemihedral twinning. This paper focuses on the utilization of noncrystallographic symmetry (NCS) averaging to solve a structure from a data set affected by perfect hemihedral twinning
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