Thanks, Garib
It might be the case.
As a matter of fact, you are welcome to look at the original data here
http://www.rcsb.org/pdb/explore/explore.do?structureId=2GL5
The data turned out to be twinned ( I also have other datasets - all
with certain degree of twinning) and now I am trying to re-refine and
then re-submit the more correct structure to the PDB.
Yury
On Thu, 10 Feb 2011, Garib N Murshudov wrote:
Maximum theoretical drop R/Rfree for perfect twin from 30% is around 25% (i.e.
it could go down to 5%). However it could only happen only if twinning is
perfect and there is no pseudo rotation parallel to twin operator.
Hypothetical case it can happen if you have refined one crystal structure at
sufficiently high resolution till (almost convergence) and another crystal is
twinned but otherwise perfectly isomorphous to the first crystal and you take
coordinates from the first crystal and refine against the second crystal.
regards
Garib
On 10 Feb 2011, at 20:14, Patskovsky Yury wrote:
Dear all,
Twin refinement has yielded Rwork/Rfree values of about 0.10/0.12 for a
nice quality 1.8A dataset (Rmerge 6%, space group I4, twin fractions 0.6/04)
and almost the same R/Rfree (0.095/0.115) for another 1.5A nice quality data
set (Rmerge 6%, space group I4, twin fractions 0.74/0.26). Refinement of
untwinned data resulted in Rfree of ~32% and ~22% respectively. REFMAC and
PHENIX both have produced the same results and almost identical R factors,
which are suspiciously VERY LOW for this resolution of data. Twin refinement
in REFMAC has produced exceptional quality maps even for 1.8A data (they look
rather like 1.2A maps) - I can not tell the same for PHENIX - maps were
looking worse (may be someone has a better idea why).
Normally twin refinement results in lowering R-factors - say, the drop in
R from 30% (without twin refinement) to 20% (with twin refinement) would be
considered normal, however we can see the drop from 32% to 12%.
I wonder if anyone else has experienced similar problems and what would
be the most reasonable explanation for that.
Thank you
Yury
Yury Patskovsky, Ph.D.
Associate,
Dept of Biochemistry
Albert Einstein College of Medicine
1300 Morris Park Ave
Bronx, NY 10461
phone 718-430-2745
yu...@medusa.vioc.aecom.yu.edu
