[phenixbb] Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees

John Pak john.pak at msg.ucsf.edu
Wed Sep 21 17:12:01 PDT 2011

Peter Zwart,

Thanks for the suggestion to try P1.

Indexing in P1 reveals the twin law "-k,-h,-l" at near 50%, as revealed 
by Xtriage.  So I will explore refining in this space group +/- twinning.

Apologies if other people have offered advice - I can only see responses 
on the phenixbb archive site at the moment!

On 20/09/2011 12:20 AM, John Pak wrote:
> Hi all,
> I currently have a dataset that scales well in C2.  (a = 224,b = 129,c 
> = 392. beta= 94.5 degrees).  Previously, I had thought that these 
> crystals were in P6322 (posted this a few months ago), but I've since 
> grown better crystals, where the beta angle is now 94.5, and not close 
> to 90.0.  I'm reasonably confident with the scaling - however, it has 
> always been really difficult to index these crystals in HKL2000.
> Like the previous crystals, this new C2 dataset looks like it might be 
> perfectly twinned, based on Xtriage's L test.
> I've solved the structure by MR, and refined it to 3.0 angstroms to 
> R=30%, Rfree=33%, but I am running out of things to fix.  I'd like to 
> perform twinning refinement, based on this Xtriage L test result.
> The problem is that Xtriage cannot find any pseudomerohedral twinning 
> laws, likely because the beta angle is too far from 90 degrees??  For 
> kicks and giggles, I started to enter arbitrary beta angles in 
> Xtriage, and at a beta angle below 93.4, Xtriage can find two twinning 
> laws (closer to 90 degrees, Xtriage can find 5 twin laws).  Using 
> "-1/2*h+3/2*k, 1/2*h+1/2*k, -l" in Phenix refine (the beta angle is 
> still 94.5 degrees, I haven't changed this) results in the R and Rfree 
> dropping a lot to 25.5 and 28.6, respectively.  Used the same random 
> seed as previous runs to generate the test set from the scalepack 
> file, with the "use lattice symmetry to generate test set" flag 
> enabled.  The maps look a lot noisier.
> So my questions are:
> 1. Is this twinning refinement valid?  I'm really thinking no - since 
> the maps didn't improve.   Suppose the maps didn't get worse though - 
> would this twinning refinement then be valid?
> 2. How do I go about reindexing this dataset in I2? i.e. to see if the 
> beta angle with this unit cell selection is closer to 90 degrees.  
> Would this even help, with respect to pseudomerohedral twinning 
> refinement?
> Thanks!

John E. Pak, Ph.D.
Postdoctoral Associate, Stroud Lab
Department of Biochemistry&  Biophysics

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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