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Hi, Assuming that the smaller protein is in the same conformation in all 6 copies, 6-fold averaging should be very powerful. If you already have a polyAla trace then the averaging will have a good mask to work from. Even at 3A, maps with nearly perfect phases show a lot of detail (cf. maps from virus structures after averaging). Averaging will work best if the 6 copies are in different orientations. It won't work as well if the copies are related by pure translations (indicated by big non-origin peaks in the native Patterson map) or if the crystal is close to possessing some higher symmetry. Best wishes, Randy Read On 4 Apr 2012, at 02:43, intekhab alam wrote:
Hi All I have a 3.0A dataset (SG P1211) of a protein-protein complex having mol.wt 60 and 8 Kda respectively. Molecular repalcement (60Kda protein as template) with Phaser gave a solution with 6 molecules in ASU. A continuous density is also obersved near two different chains which i consider as the second protein. I refined the density using a poly Alanine model but still i can't recognise the side chains confidently for modelling. Considering the fact that the smaller protein partner is rich in lysine, arginine, Asp and Glutamate with only 3 tyr and 4 phe, i tried to modell fragments one by one but the B-factor of the segments are quite high (in the range of 110) what will be the best strategy to improve the map for modelling.
regards
-- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
------ Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills Road E-mail: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk