[phenixbb] Need help in refining my twinned P6322(apparent) dataset

[Francis E Reyes]

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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---------------------------------------------
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder

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