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Re: [ccp4bb] an over refined structure |
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CCP4bb navigationCCP4bb <-- 2008 <-- February 2008 <-- 08 February 2008Subject: Re: an over refined structure From: Sue Roberts suer {- at -} EMAIL {- dot -} ARIZONA {- dot -} EDU Date: 2008-02-08 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 |
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