On Apr 1, 2009, at 7:12, conancao wrote:
Dear All:
Hi. I have a question about selecting weighing term during
restrained refinement using Refmac5 of CCP4 packages.
For a 300kDa homodimer protein structure at 2.5A, 91%
complete. I obtain optimal R and Rfree by using NCS tight restraints
of the peptides of the two monomers. Weighing term 0.15 gives
(R=0.22, Rfree=0.28) and weighing term 0.1 gives(R=0.23,
Rfree=0.28). Higher weighing term gives larger difference between R
and Rfree.
Is there a criteria or special range of choosing weighing
term? Is weighing term 0.1 too small? I read the references by Ian
Tickle (Acta Cryst D, 1998 and 2000)on R and Rfree ratio, those
helped a lot but I still do not know the key of weighing term.
The absolute value of the weighing term is rather irrelevant - it has
no physical meaning.
A term of 0.1 for 2.5 A data sounds about right in my experience, and
from what you say.
What you could try to do is to play a bit with the Bweight as well
(look at ccp4i under the Restraints panel).
At 2.5 you might want to try and relaxing NCS restraints (use medium
or exclude some regions that have a reason to be different, if they
are eg in a different crystal contact environment in each copy) and
see if they lower the Rfree. I also presume you use TLS.
Tassos
Thanks so much.
Best,
Hongnan Cao
Biochemistry Department
UC Riverside
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