| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | | |
|
|
Re: [ccp4bb] an over refined structure |
|
CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008Subject: Re: an over refined structure From: Ronald E Stenkamp stenkamp {- at -} U {- dot -} WASHINGTON {- dot -} EDU Date: 2008-02-08 symmetry space groups. When you make the NCS operators into crystallographic operators, you don't change the refinement much, at least in terms of structural changes. That's the case whether NCS restraints have been applied or not. In the cases I've re-done, changing the refinement program and dealing with test set choices makes some difference in the R and Rfree values. One effect of changing the space group is whether you realize the copies of the molecule in the lower symmetry asymmetric unit are "identical" or not. (Where "identical" means crystallographically identical, i.e., in the same packing environments, subject to all the caveats about accuracy, precision, thermal motion, etc). Another effect of going to higher symmetry space groups of course has to do with explaining the experimental data with simpler and smaller mathematical models (Occam's razor or the Principle of Parsimony). Ron On Fri, 8 Feb 2008, Sue Roberts wrote: > Back in the old days, when I worked on crystal structures with 15 or 20 > atoms or so, the symptoms of missed crystallographic symmetry included > instability of the refinement, high correlations between parameters, and > (relatively) large deviations between equivalent bond distances and bond > angles. There can be real consequences of missing symmetry and divergences > between copies of molecules, even when resolution and data quality were not > an issue, because the refinement can become unstable. Hence, I'm always > skeptical of the assumption that structures can be safely refined in space > groups of too low symmetry. I've assumed that, when people chose to (or > accidently) refine protein structures in lower symmetry space groups, > geometrical and NCS restraints keep the refinement under control. Is there > a publication somewhere that has looked at the effect of deliberate > refinement in space groups of lower than correct symmetry? > > Sue > > > On Feb 8, 2008, at 11:07 AM, Edward Berry wrote: > >> Dirk Kostrewa wrote: >>> Dear Dean and others, >>> Peter Zwart gave me a similar reply. This is very interesting >>> discussion, and I would like to have a somewhat closer look to this to >>> maybe make things a little bit clearer (please, excuse the general >>> explanations - this might be interesting for beginners as well): >>> 1). Ccrystallographic symmetry can be applied to the whole crystal and >>> results in symmetry-equivalent intensities in reciprocal space. If you >>> refine your model in a lower space group, there will be reflections in >>> the test-set that are symmetry-equivalent in the higher space group to >>> reflections in the working set. If you refine the (symmetry-equivalent) >>> copies in your crystal independently, they will diverge due to >>> resolution and data quality, and R-work and R-free will diverge to some >>> extend due to this. If you force the copies to be identical, the R-work >>> & R-free will still be different due to observational errors. In both >>> cases, however, the R-free will be very close to the R-work. >> > > Sue Roberts > Biochemistry & Biophysics > University of Arizona > > suer@email.arizona.edu > CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008 |
| ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd |