[phenixbb] Pseudo-merohedral twinning refinement in C2, when beta = 94 degrees
john.pak at msg.ucsf.edu
Wed Sep 21 17:12:01 PDT 2011
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
John E. Pak, Ph.D.
Postdoctoral Associate, Stroud Lab
Department of Biochemistry& Biophysics
Genentech Hall Room S414
San Francisco, CA 94158-2517
Lab #: 415-476-3937
Fax #: 415-476-1902
Cell #: 415-215-0048
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