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
[EMAIL PROTECTED]
