Open AccessDetection and correction of underassigned rotational symmetry prior to structure deposition
Author(s) -
Poon Billy K.,
GrosseKunstleve Ralf W.,
Zwart Peter H.,
Sauter Nicholas K.
Publication year - 2010
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444910001502
Subject(s) - symmetry (geometry) , rotational symmetry , molecular symmetry , symmetry operation , protein subunit , group (periodic table) , protein data bank , crystallography , protein data bank (rcsb pdb) , space (punctuation) , diffraction , protein structure , computer science , mathematics , algorithm , physics , geometry , chemistry , optics , nuclear magnetic resonance , quantum mechanics , molecule , biochemistry , gene , operating system
Up to 2% of X-ray structures in the Protein Data Bank (PDB) potentially fit into a higher symmetry space group. Redundant protein chains in these structures can be made compatible with exact crystallographic symmetry with minimal atomic movements that are smaller than the expected range of coordinate uncertainty. The incidence of problem cases is somewhat difficult to define precisely, as there is no clear line between underassigned symmetry, in which the subunit differences are unsupported by the data, and pseudosymmetry, in which the subunit differences rest on small but significant intensity differences in the diffraction pattern. To help catch symmetry-assignment problems in the future, it is useful to add a validation step that operates on the refined coordinates just prior to structure deposition. If redundant symmetry-related chains can be removed at this stage, the resulting model (in a higher symmetry space group) can readily serve as an isomorphous replacement starting point for re-refinement using re-indexed and re-integrated raw data. These ideas are implemented in new software tools available at http://cci.lbl.gov/labelit.