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Acta Crystallographica Section D Biological Crystallography, volume 70, issue 9, pages 2430-2443

Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda

Lebedev Andrey A. 1
Isupov Michail N. 2
1
 
CCP4, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0FA, England
2
 
Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Stocker Road, Exeter EX4 4QD, England
Publication typeJournal Article
Publication date2014-08-29
Quartile SCImago
Quartile WOS
Impact factor
ISSN09074449, 13990047
General Medicine
Structural Biology
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 andvice versa. A mistake only becomes apparent when theRfreeceases 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 programZanudapresented in this article was developed for the automation of SG validation.Zanudaruns 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.

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Lebedev A. A., Isupov M. N. Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda // Acta Crystallographica Section D Biological Crystallography. 2014. Vol. 70. No. 9. pp. 2430-2443.
GOST all authors (up to 50) Copy
Lebedev A. A., Isupov M. N. Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda // Acta Crystallographica Section D Biological Crystallography. 2014. Vol. 70. No. 9. pp. 2430-2443.
RIS |
Cite this
RIS Copy
TY - JOUR
DO - 10.1107/S1399004714014795
UR - https://doi.org/10.1107%2FS1399004714014795
TI - Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda
T2 - Acta Crystallographica Section D Biological Crystallography
AU - Lebedev, Andrey A.
AU - Isupov, Michail N.
PY - 2014
DA - 2014/08/29 00:00:00
PB - International Union of Crystallography (IUCr)
SP - 2430-2443
IS - 9
VL - 70
SN - 0907-4449
SN - 1399-0047
ER -
BibTex |
Cite this
BibTex Copy
@article{2014_Lebedev
author = {Andrey A. Lebedev and Michail N. Isupov},
title = {Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda},
journal = {Acta Crystallographica Section D Biological Crystallography},
year = {2014},
volume = {70},
publisher = {International Union of Crystallography (IUCr)},
month = {aug},
url = {https://doi.org/10.1107%2FS1399004714014795},
number = {9},
pages = {2430--2443},
doi = {10.1107/S1399004714014795}
}
MLA
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MLA Copy
Lebedev, Andrey A., and Michail N. Isupov. “Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the programZanuda.” Acta Crystallographica Section D Biological Crystallography, vol. 70, no. 9, Aug. 2014, pp. 2430-2443. https://doi.org/10.1107%2FS1399004714014795.
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