Re: [ccp4bb]: How to deal with sidechainatoms with low electron density?

[Pawel Dokurno <pdokurno@ribotargets.com>]

Much easier, and more informative, would be setting occupancy factors
to 0.01 for these disordered atome. It enables atom to be moved by
refinement programs, but its contribution into calculated structure
factors (and maps) is 100 times lower, i.e. negligible. So its positions
are only defined by geometry libraries.

Pawel
 

Dirk Kostrewa wrote:

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On Friday 22 November 2002 13:35, Florian Schmitzberger wrote:
> Dear all,
>
> I was wondering what the most acceptable way to deal with (disordered)
> sidechains/residues (e.g. sidechains of Arginines and Lysines) with very
> low or no electron density is? Especially with respect to submission of
> coordinates to the pdb-data bank.
>
> My initial approach was to set the occupancies of the atoms to 0 and
> then refine in Refmac. However I encountered that the geometry (bond
> lenghts and angles) gets distorted between the atoms with normal
> occupancy and the ones with zero occupancy. The other option to refine
> the residues as alanines does not seem a very good idea to me, since it
> does not account for something which is there, but strongly disordered.
> For me the most ideal way to deal with them is to fix the B-factor to a
> very high value and then refine with Refmac.
>
> What is the general opinion about this matter?
>
> I would be grateful for any comments.
>
>
> Thank you,
>
>
> Florian
>
> -------------------------------------
> Florian Schmitzberger
> University of Cambridge
> Department of Biochemistry
> 80 Tennis Court Road
> CB2 1GA Cambridge
> Tel: 0044-1223-766029

Dear Florian,

in my opinion, the worst treatment is to replace disordered side chains like
Lys, Arg, Glx by alanine, because this doesn't correspond to the true amino
acid sequence. Of the other two possibilities, occupancies=0 or occs=1 with
very high B-factors, I prefer the latter one, simply because most other
people working with structures do not have access to the electron density and
thus usually judge the quality of residues by their B-factors. Another reason
for me is that an occupancy of 0 for one conformation is unphysical, and you
can't model an arbitrarily high number of conformations with Occs close to
zero (because of inflation of refinable parameters). A very high B-factor
effectively smears the conformation of that side chain over a large volume
which is what you want. However, its contribution to the model's lower
resolution structure factors may be somewhat overestimated compared to a
large number of different conformations that sum up to 1, but protein
structures aren't perfect, anyway.

Best regards,

Dirk.

--

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Dirk Kostrewa
Paul Scherrer Institut
Life Sciences, OSRA/007
CH-5232 Villigen PSI, Switzerland
E-mail: dirk.kostrewa@psi.ch
Phone: +41-56-310-4722
Fax: +41-56-310-4556
WWW: http://www.sb.psi.ch
****************************************

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