Quoting you:
"I wish to solve a monomeric protein in P21 where there are 2 monomers in asymmetric unit."
How do you know that if you haven't solved the structure? Matthews coefficient calculations?
Remember that the solvent content in protein crystal structures can go from ca. 15 % to ca. 85 %.
So what about having only one monomer in the asymmetric unit? What are the statistics given by Phaser then? Does the molecular replacement solution provided by
Phaser for just one monomer explain the crystal (i.e. contacts in all 3 directions of space so that the crystal can form, no "void" between rows of molecules).
The second possibility is having different orientations of surface loops (these surface loops would be clashing), so that you may have to trim them off before performing
the molecular replacement calculations. Then you need to use the (improving) electron density in order to rebuild the surface loops in their correct positions.
HTH,
Fred.
(there are other possibilities of course, such as incorrect space group assignment)
> Message du 15/03/11 07:41
> De : "Careina Edgooms"
> A : [log in to unmask]
> Copie à :
> Objet : [ccp4bb] molecular replacement solution
>
> Dear CCP4 members
>
> I have a confusion with molecular replacement. I wish to solve a monomeric
> protein in P21 where there are 2 monomers in asymmetric unit. I have a search
> model that also has 2 monomers in asymmetric unit.
>
>
> First I try using Phaser. I use only one chain of the monomer model and search
> for 2 copies. This gives a good solution that refines with low R-factor but it
> shows many clashes. In other words, the 2 monomers are too close together and
> there are clashes where they meet. Then I try using Phaser and both chains of
> the model and search for 1 copy. This does not give a solution and says
> asymmetric unit is too full. Then I try using MolRep with the 2 chain search
> model. It gives solution that looks better because you can see that the 2
> monomers do not physically clash but it refines very badly giving R factors of
> about 50%
>
> So I am confused. What am I doing wrong? Please help me with suggestions
> Many thanks
> Careina
>
>
>
>
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