Pat,
Try TLS - I usually don't invoke it at this type of resolution but in
one case I saw it make a surprisingly significant improvement.
I would also be tempted to put the structures through Arp/wArp and see
if it lowers the R-free any more - rightly or wrongly I view this as the
lowest reasonably achievable R-factor with isotropic modeling - and
especially look at the maps after it has finished in case it shows up
anything you had missed.
When I had P21 -> P2x212x twinning the R-free held up in the mid-30's at
2 Angstrom resolution so absent any indications in Truncate or Xtriage I
wouldn't suggest that.
A final question is how much disordered structure is missing from your
models ? Could a partly ordered but unmodeled segment be driving up
R-free ?
Cheers
Phil Jeffrey
Princeton
On 4/26/13 5:38 PM, Patrick Loll wrote:
Hi all,
Here is a problem that's been annoying me, and demanding levels of thought all
out of proportion with the importance of the project:
I have two related crystal forms of the same small protein. In both cases, the
data look quite decent, and extend beyond 2 A, but the refinement stalls with
statistics that are just bad enough to make me deeply uncomfortable. However,
the maps look pretty good, and there's no obvious path to push the refinement
further. Xtriage doesn't raise any red flags, nor does running the data through
the Yeates twinning server.
Xtal form 1: P22(1)2(1), a=29.0, b=57.4, c=67.4; 2 molecules/AU. Resolution of
data ~ 1.9 Å. Refinement converges with R/Rfree = 0.24/0.27
Xtal form 2: P2(1)2(1)2(1), a=59.50, b=61.1, c=67.2; 4 molecules/AU. Resolution
of data ~ 1.7 Å. Refinement converges w/ R/Rfree = 0.21/0.26
As you would expect, the packing is essentially the same in both crystal forms.
It's interesting to note (but is it relevant?) that the packing is quite
dense--solvent content is only 25-30%.
This kind of stalling at high R values smells like a twin problem, but it's not
clear to me what specific kind of twinning might explain this behavior.
Any thoughts about what I might be missing here?
Thanks,
Pat
---------------------------------------------------------------------------------------
Patrick J. Loll, Ph. D.
Professor of Biochemistry & Molecular Biology
Director, Biochemistry Graduate Program
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA 19102-1192 USA
(215) 762-7706
pat.l...@drexelmed.edu
