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NAD & b-factors > 100 A2

Yoram Puius puius at aecom.yu.edu
Mon Jul 21 17:35:57 EST 1997

Jordi Benach wrote:
> When I do group b-factor refinement of the NAD+ molecule, the value
> gets about 100 A2? If I try individual b-factor refinement -only for
> the NAD+ molecule- some atoms get as well 100 A2 as b-factor.
> Could someone give me a hint?
> Cheers,
> JB

My first guess would be partial occupancy of the NAD+, i.e. it's not
present in every unit copy of your protein in the crystal.  One thing
you can try to do is set all the B=20.0 or so in the NAD+ and do
a group occupancy refinement (feel free to ask me on how to do this
if you have trouble).

As for the problems with positional refinement.... I dunno.  If you
are keeping the protein fixed while refining the NAD+, maybe that's
now allowing the protein to be tweaked to accomodate the cofactor,
If that is not the case, I don't know.

As an experiment, try using the old atom names.  You can always rename
stuff every cycle before entering O, although that is a pain.

	- Y

Yoram A. Puius                Albert Einstein College of Medicine
6th year M.D.-Ph.D.           Department of Biochemistry
mailto:puius at aecom.yu.edu     1300 Morris Park Avenue, Bronx, NY  10461
   "I get more work done every week than you do in a day!"

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