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I would like to reinforce Randy's suggestion about looking at relatives/structurally similar proteins that have less sequence identity and superimposition to find a common core or set of models. In this context, also try using FFAS (http://ffas.sanfordburnham.org/ffas-cgi/cgi/ffas.pl), which have found to be very useful. Thanks, Debanu On Thu, Jul 7, 2016 at 8:34 AM, Vandna Kukshal <[log in to unmask]> wrote: > I will try this approach. there are two PDB with 28 % and 26 % identities > and fold is identical with many other its relatives. > -Vandna > > On Thu, Jul 7, 2016 at 2:38 AM, Randy Read <[log in to unmask]> wrote: >> >> Hi, >> >> Others have made a lot of good suggestions. There's one other thing I was >> wondering about. I don't think you've mentioned whether you had a number of >> choices of model in the PDB. If there are other relatives, even if the >> sequence identity is lower, you should remember that sequence identity isn't >> a perfect predictor of model quality. One of the other models with lower >> sequence identity might turn out to be better. Alternatively, looking at >> the superposition of a set of possible models might give you a hint about >> potential conformational variability, so that you could trim your model down >> to a conserved core. >> >> Good luck! >> >> Randy Read >> >> On 7 Jul 2016, at 00:13, Vandna Kukshal <[log in to unmask]> wrote: >> >> Hi, >> I am trying to solve one structure with MR and got stucked with no >> solution. I have 2.7 A data , i indexed with P3 and Spacegroup what >> pointless gave me is P622. cell dimention is 68 , 68, 348. Data looks good >> with R merge ~0.012 and Chi2~1. >> Mathew coefficient shows 2-3 molecules in assymetric unit. protein exist >> as dimer or as tetramer. >> I have model with 28 % identity , i tried MR with all the possible >> spacegroups of P622 but tfz was ~ 5- 6 . I searched for 2-3 monomer as >> well as 1 dimer. >> in this protein i have only 1 methionine (115 a.a long protein). >> >> Any suggestion about solving this problem. >> thanks >> >> . >> -- >> Vandna Kukshal >> Postdoctral Research Associate >> Dept. Biochemistry and Molecular Biophysics >> Washington University School of Medicine >> 660 S. Euclid, Campus Box 8231 >> St. Louis, MO 63110 >> >> >> ------ >> 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: [log in to unmask] >> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk >> > > > > -- > Vandna Kukshal > Postdoctral Research Associate > Dept. Biochemistry and Molecular Biophysics > Washington University School of Medicine > 660 S. Euclid, Campus Box 8231 > St. Louis, MO 63110