Hi Pat,
On top of Phil's suggestion for invoking TLS, what about the NCS? Is there
anything peculiar about them (tNCS or the like)? If there isn't, are you
imposing NCS during refinement? perhaps you should relax the NCS restraints or
not impose any at all and see what happens then?
My 2p thoughts.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710
________________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Patrick Loll
[pat.l...@drexel.edu]
Sent: Saturday, April 27, 2013 12:38 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] refinement hanging--what am I missing?
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
