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Hi Phoebe,
Parallel NCS and crystallographic symmetry leads to translational
symmetry and systematic weakening and strengthening of reflections (in
special pseudosymmetry cases it can for instance mimic a centered space
group). I expect that if you just place two monomers with the proper
translational symmetry then you will get a strong correlation between
Fcalc and Fobs and a below-random R-factor even if the model has major
errors. This would apply to both Rwork and Rfree. Thin shells won't help
in this situation and because other basic assumptions about intensity
distributions is violated, ML refinement may not behave as expected either.
Bart
[EMAIL PROTECTED] wrote:
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Not all cases of NCS undermine Rfree: There are many where the NCS
axis is roughly parallel to an xtal symmetry axis - e.g. P61 with a
non-xtal twofold running nearly parallel to the xtal 6fold screw, so
that NCS-related reflections are already xtal-symmetry - related. I
don't see how the NCS can affect Rfree in such cases?
Phoebe
At 02:49 PM 12/29/2006, Jan Abendroth wrote:
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A way to avoid biasing Rfree values is to choose the test set in
thin resolution shells whenever NCS is present. Currently, this
precaution is often ignored. It should become a de facto standard
for publication of structures containing NCS.
Hi all,
btw - it would be fantastic and certainly would encourage us to use
it more often if the assignment of free reflections in resolution
shells was incorporated in a ccp4 program. Yes, one can for instance
go through shelxpro, however if one wants to go back to ccp4 this
route is a bit painful.
Cheers
Jan
--
Jan Abendroth
University of Washington
Institute of Biochemistry
1959 NE Pacific Street, K-426
Box 357742
Seattle, WA-98195
phone: +1-206-616-4510
fax: +1-206-685-7002
---------------------------------------------------------------------------------------------------------------------------
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
fax 773 702 0439
http://bmb.bsd.uchicago.edu/index.html
http://www.nasa.gov/mission_pages/cassini/multimedia/pia06064.html
