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Space-Group and Origin Ambiguity in Macromolecular Structures with Pseudo-Symmetry and its Treatment with the Program Zanuda

DOI: 10.1107/S1399004714014795 DOI Help
PMID: 25195756 PMID Help

Authors: Andrey Lebedev (Science and Technology Facilities Council (STFC)) , Misha Isupov (University of Exeter)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acta Crystallographica Section D Biological Crystallography , VOL 70 , PAGES 2430 - 2443

State: Published (Approved)
Published: September 2014
Diamond Proposal Number(s): 8889 , 6851

Abstract: The presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the Rfree ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics.

Subject Areas: Biology and Bio-materials

Instruments: I24-Microfocus Macromolecular Crystallography

Added On: 07/10/2014 12:01

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