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Re: [ccp4bb] Commensurate superlattices in protein crystallography? |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 15 March 2007Subject: Re: Commensurate superlattices in protein crystallography? From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN Date: 2007-03-15 I think it may necessary to collect all satellites corresponding to the 256 Angstrom axis in order to solve the structure correctly. In small-molecular crystallography there is already straightforward way of solving superstructures: Derive phases of main reflections (corresponding to 64 Angstroms axis in this case) by whatever manner without building any structure models, then derive phases of satellites by a modified Sayre¡¯s equation making use of the known phases of main reflections. I think the same principle is also applicable to proteins although there are no programs available yet for this purpose. Regards, Hai-fu Professor Fan, Hai-fu Institute of Physics Chinese Academy of Sciences Beijing 100080, P.R. China E-mail: fanhf@cryst.iphy.ac.cn URL: http://cryst.iphy.ac.cn _____ From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of John R Helliwell Sent: 2007Äê3ÔÂ16ÈÕ 0:31 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Commensurate superlattices in protein crystallography? Dear Colleagues, I am currently engaged analysing a protein crystal structure which has two unusual aspects about it, at least to me (hence this consultation). The first oddity is the unit cell and space group:- Triclinic P1 64.43 70.81 79.26 89.83 110.95 116.59 ie note the value of alpha very near 90 degrees. Autoindexing does offer a C2 space group solution but, on inspection, is clearly too far from a proper prediction. A complication that follows from the triclinic alpha near 90 degrees is the setting of the crystal and the indexing within P1 can need altering (Phil Evans' initiative with 'pointless' solved that; thanks to Eleanor for a pre-release alert of this software). Taking the analysis through to a 2 derivative electron density map, with DM, was apparently fine but the electron density connectivity was too poor to develop. I thus went back to the diffraction patterns, image by image. This led to the second oddity, now I believe truly odd:- Second oddity:- some diffraction images showed a superlattice effect. These can be neatly predicted through a doubling of the 'a'' unit cell value to 128Angstrom. This is an example of a commensurate lattice. Some of this subset of images show a quadrupling superlattice ie where spots are explained on a prediction of 256Angstrom for the 'a' value. Maps based on '2a' might be ok to develop but still look 'difficult' to me re electron density connectivity. An analysis based on '4a' is confounded by the prediction showing nearly all spots as overlaps ie detector too close and rotation angle too wide for a 256 Angstrom axis. My checking of the IUCr Journals literature yields an example of an incommensurate superlattice:-(J. Appl. Cryst. (2004). 37, 327-330 [ ] Imaging modulated reflections from a semi-crystalline state of profilin:actin crystals Do colleagues on CCP4bb have similar examples and did they manage to progress to a structure? Best wishes and thankyou, John -- John R Helliwell Professor of Structural Chemistry, The University of Manchester; CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 15 March 2007 |
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