In such cases, we always define the test set first in the high-symmetry
space group choice. Then, if it is warranted to lower the
crystallographic
symmetry and replace with NCS symmetry, we expand the test set
to the lower symmetry space group. In other words, the test set itself
will be invariant upon applying any of the crystallographic or NCS
operators,
so will be maximally "free" in these cases. It is then also possible
to
directly compare the free R between the high and low crystallographic
space group choices.
Our recent Neuroligin structure is such an example (Arac et al.,
Neuron 56, 992-, 2007).
Axel
On Feb 8, 2008, at 10:48 AM, Ronald E Stenkamp wrote:
I've looked at about 10 cases where structures have been refined in
lower
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
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atb.slac.stanford.edu
Email: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
