---------- Forwarded message ---------- From: "Van Den Berg, Bert" To: "PHENIX user mailing list" Date: Tue, 15 Mar 2011 08:01:42 -0400 Subject: Hi John, How do the maps look for cases 3 and 4? Are they great or are there obvious things to correct? Does your model have the correct sequence or is it that of the search model? I’m asking because your R’s seem reasonable to me after a first round of refinement and using a 30% identical search model for MR. So maybe there is no problem? Bert On 3/15/11 2:55 AM, "John Pak" wrote: Hey Phenix community, Here are the details of my current situation - any assistance in the matter would be greatly appreciated as I've been struggling mightily for the past month trying to get this structure refined (to no avail). Details: -3.0 angstrom dataset from a membrane protein crystal -reduced in a P3 Bravis lattice using HKL2000 -Pointless and Xtriage suggest P622 symmetry -Solved structure via MR - ran Phaser in all P622 based space groups, found 1 convincing solution in P6322 (LLG ~110) which makes biological sense (1 monomer in ASU that lies on the screw axis to recapitulate the biological trimer) -31% sequence identical search molecule -no pseudotranslation (via Xtriage) Xtriage suggests that the P6322 dataset is nearly perfectly twinned (twin fraction = 0.49).  Mindful of the fact that there are no twin operators for P6322, I'm thinking that the true space group is P321, P312 or P63 and I've tried a number of things listed below: 1.  Refined in P6322 (simulated annealing+individual B).  Missing side chains and incorrectly modelled loops apparent in maps.  Start R=0.49, Rfree=0.5. Refinement stalls at R=0.41, Rfree=0.45 after building. 2.  Ran Phaser in P312 (using unrefined model) - no solution. 3. Ran Phaser in P321 (using unrefined model).  One nice solution (LLG ~220) - lattice looks very similar to P6322 crystal packing.  Twin refinement in phenix using operator suggested by Xtriage (simulated annealing + individual B) results in R=0.38, Rfree=0.41 (no rebuilding performed). 4. Ran Phaser in P63 (using unrefined model).  Three solutions (LLGs all ~210) - solution #3 looks very similar to P6322 crystal packing.  Twin refinement in phenix using operator suggested by Xtriage of solution #3 gives R=0.37, Rfree=0.40 (no rebuilding performed).  Solutions #1 and #2 do not give packing arrangements that look like the P6322 solution. Twin refinement of Sol 1 and 2 give higher R factors. So I'm at a loss as to which space group my crystal truly belongs to, and where I should be focusing my refinement.  The maps all look similar before and after DM. Thanks for any assistance or recommendations that you might have! -- John E. Pak, Ph.D. Postdoctoral Associate, Stroud Lab Department of Biochemistry&  Biophysics UCSF MC2240 Genentech Hall Room S414 600-16th St. San Francisco, CA 94158-2517 Lab  #: 415-476-3937 Fax  #: 415-476-1902 Cell #: 415-215-0048