Re: [ccp4bb]: ligands in a 2-fold axis

["Eleanor J. Dodson" <ccp4@ysbl.york.ac.uk>]

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Rongsheng Jin wrote:
> 
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> 
> Hi there,
> 
> My protein crystallized in the P21212 space group. It forms a homo-dimer
> around the crystallographic 2-fold axis. There is one small molecule
> ligand binds to each protomer. The interesting thing is that the 2-fold
> axis goes through the middle of the ligand molecules, although the
> ligand itself is not perfectly 2-fold symmetric. It ends up with two
> ligands overlap with each other while the 2-fold axis goes in the middle.
> Does anybody know how to do the refinement (CNS?) without reducing to the
> p21 space group?
> 
> Thanks,
> 
> Rongsheng


 First - if this is happened your spacegroup is not P21212 - it is P21
with an NCS axis relating the two protein molecules..

 You must first process the data with P2/m symmetry - 
once you have merged h k l and -h -k l you have lost the information
about the ligand orientation. (lets hope you collected enough redundant
data to cover the larger asym unit!!)

 Then impose NCS restraints on the protein and look for the ligand in
the diff map..

Eleanor 

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Eleanor J.Dodson, York Structural Biology Laboratory,
                  Chemistry Department, 
                  University of York, Y01 5DD Heslington, U.K.
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