John, Have you tried Zanuda to resolve the space group ambiguity? F On Mar 15, 2011, at 12:55 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
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