Thank you Jacob and Ethan! I haven't put water molecules into the density blob, which aren't many out there, but I fitted the ligands in already. Molbrobity statistics are not yet great, since there are 13.5% rotamer outliers.
Will adjust the models manually, and try refmac and TLS refinement. Thanks again for your insightful suggestions! Best, Mengbin On Wed, Jun 10, 2015 at 6:16 PM, Ethan A Merritt <merr...@u.washington.edu> wrote: > On Wednesday, 10 June, 2015 17:35:25 Mengbin Chen wrote: > > Hello everyone, > > > > I am refining a 2.5 angstrom structure whose phase is solved by molecular > > replacement with a search probe determined by SAD with 3 angstrom > > resolution. While I am able to see densities of a bunch of water > molecules > > and ligands in the MR solved structure, which means that the phase is > > correct, the Rfree gets stuck at ~27%. > > Why do you think this is a problem? > It is true that turning on twin refinement is expected to yield lower > R factors, and thus 27% in the presence of twin refinement is worse than > 27% without twin refinement. But having said that, Rfree = 0.27 is still > not so horrible. > > If the starting point for your MR solution was a 3A model, > there may have been errors in sidechain placement or even > backbone conformation that can be corrected now that you > have higher resolution data. Don't assume that the starting > model was perfect. > > You say that you can see density for a bunch of waters and ligands. > Are these in your refinemed model yet? > > What does Molprobity (or coot or phenix) say about the quality of > your sidechain rotamers? > > Have you tried adding a TLS description? > > Ethan > > > > The crystal belongs to P3221 and has > > a twinning fraction of 19%, according to Xtriage. Currently I've been > > sticking to Phenix for refinement, and twin law (-h, -k, l) has been > > applied. > > > > I was wondering if the CCP4 community would have any suggestions of how > to > > refine this twinned structure, such as softwares to use, tricky > strategies > > to choose, etc. I really appreciate any recommendations you would come up > > with my situation! > > > > Thank you in advance! > > > > Best, > > Mengbin > > > > > -- > Ethan A Merritt > Biomolecular Structure Center, K-428 Health Sciences Bldg > MS 357742, University of Washington, Seattle 98195-7742 > > -- Mengbin Chen PhD Candidate Christianson Laboratory Department of Chemistry University of Pennsylvania 231 S. 34th Street, #323 Philadelphia, PA 19104 USA Phone: (215)898-2227 Email: mengb...@sas.upenn.edu
