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
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