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Hi Bart,
I've puzzled about this quite a bit and I don't think its always true.
Our non-xtal, fairly imperfect 2fold is actually more-or-less coincident
with the xtal 61 screw, and doesn't create pseudo-translational
symmetry. It IS very-very-pseudo-P6122, but the "twofolds" perpendicular
to the 61 screw are only even nominally obeyed by one of two protein
domains (and if I remember correctly, processing in the higher-symmetry
spacegroup gave essentially random merging statistics).
This is a valuable discussion though because more and more of these
funky pseudo-symmetry problems seem to crop up, at least in my lab. And
its far more interesting than what I'm supposed to be working on in the
office ...
Phoebe
At 11:17 AM 12/30/2006, Bart Hazes wrote:
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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
---------------------------------------------------------------------------------------------------------------------------
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
