5AOO

X-ray structure of a human Kobuvirus: Aichi virus A (AiV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.330 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The Use of Noncrystallographic Symmetry Averaging to Solve Structures from Data Affected by Perfect Hemihedral Twinning

Sabin, C.Plevka, P.

(2016) Acta Crystallogr.,Sect.F 72: 188

  • DOI: 10.1107/S2053230X16000923

  • PubMed 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. I ...

    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.


    Organizational Affiliation

    Central European Institute of Technology - Masaryk University, Kamenice 653/25, 625 00 Brno, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VP0
A
253Aichi virus (strain Human/A846/88/1989)Mutation(s): 0 
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Go to UniProtKB:  O91464
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
VP1
B
370Aichi virus (strain Human/A846/88/1989)Mutation(s): 0 
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Go to UniProtKB:  O91464
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
VP3
C
223Aichi virus (strain Human/A846/88/1989)Mutation(s): 0 
Find proteins for O91464 (Aichi virus (strain Human/A846/88/1989))
Go to UniProtKB:  O91464
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Work: 0.330 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 350.816α = 90.00
b = 350.816β = 90.00
c = 350.816γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOLREPphasing
XDSdata reduction
GLRFphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2017-04-05
    Type: Refinement description