you didnt by any chance mix up Rfree and the rest of the data flags at
any point...??? (that wouldnt probably explain the low Rfree value
though...)
unless you then mix them up again mid -way through... check your
flags? (1 or 0)
tommi
On Feb 10, 2011, at 11:36 PM, 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
Tommi Kajander, Ph.D.
Structural Biology and Biophysics
Institute of Biotechnology
University of Helsinki
Viikinkaari 1
(P.O. Box 65)
00014 Helsinki
Finland
p. +358-9-19158903
tommi.kajan...@helsinki.fi
