Just a warning: When doing twin refinement (and in general) you should always use original data for refinement. After refinement data may be different (in case of twin de-twinned).
I will have a look as soon as I have some time. regards Garib On 10 Feb 2011, at 22:06, Patskovsky Yury wrote: > 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 >>> [email protected] >> >>
