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[ccp4bb]: RE: Disorder about a crystallographic twofold

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Dear Manfred,

I've got a crazy idea, maybe it will work. I think you are right to refine the
disordered half-dimer (protomer) with two copies each with 0.5 occupancy. From
your Molcular Replacement solution, this seems to be an appropriate assumption.
The problems, of course, are that you introduce a large number of refinable
parameters, and that your mixture of electron density maps is probably hardly
interpretable. In this case, I would suggest the following: define for each of
the two half-occupied protomers the non-crystallographic symmetry operator to
one of the fully occupied protomers of your full dimer (your two distinct MR
solutions already indicate this!). Then, refine each of the disordered
protomers by applying either strict NCS constraints or tight NCS restraints to
its related well-defined protomer of the full dimer. I think, this would be
justified by your two MR solutions and it will reduce somewhat the number of
refineable parameters. You may optimize your NCS refinement by looking at the
free-R, although strictly spoken, it will not be "free", anymore because of
introducing an NCS relationship and because of optimizing the relative weights,
but anyway, I believe, the NCS refinement would be a much safer than to
individually refine your disordered protomer.

Good luck,

Dirk Kostrewa.

Manfred Weiss wrote:

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> Dear colleagues,
> I am working on a crystal structure in space group C2 that
> contains three molecules in the asymmetric unit. The functional
> unit of the protein is a dimer, and consequently I find 1.5 dimers
> in the asymmetric unit. The complete dimer is well defined in the
> electron density, but the half dimer seems to be disordered about
> the crystallographic twofold axis.
> Molecular replacement gave two solutions for the half dimer in the
> rotation, approximately 30 degrees apart. Each of the two solutions
> refines alright together with the complete dimer, but the refinement
> gets stuck at about R=29% and Rfree=33% (resolution 1.9 A) and the
> electron density for the half dimer looks ok for about 30% of the
> molecule and pretty bad for the rest. If I refine the complete dimer
> together with both half dimer coordinate sets at occupancies of 0.5
> for both orientations, the structure refines to R=24% Rfree=30%, so
> there seems to be some information in both solution. Of course the
> electron density does not look great still.
> My question is, has anybody encountered a similar problem, or does
> anybody know of a paper dealing with such a thing? And how do you
> deal with this? I could of course just forget about the disordered
> half dimer, and describe just the well-ordered dimer, but I'd prefer
> to do a proper job.
> By the way, the data scale well, the merging R is about 4% overall
> with an I/sigma of about 3.0 at the high resolution end, and a
> data redundancy of about 4.5.
> Any hint is appreciated.
> Cheers, Manfred.
> --
>  Manfred S. Weiss, Dr.
>  Institute of Molecular Biotechnology
>  Department of Structural Biology and Crystallography
>  Beutenbergstrasse 11                                 Fon: +49-3641-65-6081
>  Postfach 100813                                      Fax: +49-3641-65-6062
>  D-07708 Jena                                    Email: msweiss@imb-jena.de
>  GERMANY                        Web: http://www.imb-jena.de/www_sbx/manfred


* Dirk Kostrewa          |                              *
* Paul Scherrer Institut | e-mail: dirk.kostrewa@psi.ch *
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