Dear Sangeetha,
before worrying about the B-factor column in your PDB file I would be
worrying about atoms not having density. This should tell you that
your model (atoms and/or parametrisation) isn't correct.
One possible reason for those high-B side-chain atoms could be a
sequence shift: sometimes the difference between neighbouring residues
could be very small in terms of atoms and constellation. Just putting
the B-factors into a numerical range you are happy with doesn't make
your model better - it still doesn't fit your density.
Same for your ligand: if you have one atom inside density with a B of
40 and the next atom bonded to that one sticks out with a B-factor of
200 ... are you sure your ligand is actually in there and has bound in
that orientation?
So I would say these high B-factors are a good thing: they show you
where your model is poor. But then: you already see those atoms
sticking out of density, so you know where you still have to improve
your model, right?
There could also be some issue with radiation damage (are those high-B
atoms on the ligand maybe I or Br?) ... decarboxylation on side-chains
etc etc.
Just some ideas ...
Cheers
Clemens
On Thu, Jan 28, 2010 at 11:04:52AM -0500, Sangeetha Vedula wrote:
> Dear all,
>
> I am refining a crystal structure with two enantiomers of the ligand lying
> on a two-fold crystallographic axis (making the density an average of 4
> orientations/optical identity). The ligand fits pretty well over all in the
> density, but some atoms stick out of density. While B-factors for the atoms
> that are within the density, the B-factors are in the range of 20-40. For
> the ones sticking out, the B-factors are 200-400. Which doesn't make
> chemical sense, as clearly, one atom isn't jumping around so much more than
> the others.
>
> Is there any way I can force refmac to make the B-factors more reasonable? I
> also notice that some side chain atoms that stick out of density have
> horrendous B-factors.
>
> Thanks in advance,
>
> Sangeetha.
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
|