Hi,
At this resolution, such a difference in Rs could be an indicator that
the structure is over--fitted.
What weight did you choose?
Lijun
On Dec 10, 2010, at 3:17 AM, Petr Kolenko wrote:
Dear colleagues,
I appreciate any help, or any suggestion with my difficult data. Many
thanks at least for consideration.
I work with datasets at 3.6AA of resolution. Integrated with XDS,
scaled with SCALA. After integration and scaling in P1, POINTLESS
suggested space group I432:
Space group confidence: 0.95
Laue group confidence: 1.000
Total probability: 0.97
After any longer refinement (more than 20 cycles), there was always a
big gap between Rwork and Rfree (0.22 and 0.33), although the
structure looks quite good at this resolution. I tried also space
group I23, here are my statistics:
Data processing (I23 vs I432):
Rmerge - 0.124 vs 0.134
high resolution Rmerge - 0.649 vs 0.732
low resolution Rmerge - 0.048 vs 0.037
The gap between Rwork and Rfree was stabilized in I23 using tight NCS
restraints:
Rwork vs Rfree:
I23 withouth NCS: 0.228 vs 0.334
I23 with NCS: 0.249 vs 0.296
I43 : 0.228 vs 0.326
My question is, what would you recommend me to close the gap? Or is
this Rfree pointing out a lower real symmetry (I23) than suggested by
POINTLESS or PHENIX.XTRIAGE (I432)? I have tried different selection
of free reflections in I432 dataset already, but with almost the same
results.
Many thanks for any response.
Petr
--
Petr Kolenko
petr.kole...@biochemtech.uni-halle.de
http://kolda.webz.cz
Lijun Liu
555 Mission Bay Blvd South
CVRB Room 482, MBox 3122
University of California, San Francisco
San Francisco, CA 94158
Phone: (415)514-2836
