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CCP4BB  February 2009

CCP4BB February 2009

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Subject:

Re: Choosing MR solutions in the case of perfect twinning with P41212?

From:

Roberto Steiner <[log in to unmask]>

Reply-To:

Roberto Steiner <[log in to unmask]>

Date:

Thu, 5 Feb 2009 18:57:47 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (71 lines)

Hi Francis,
I would consider the possibility of a orthorhombic sg (a~b with  
twinning).  If unlucky maybe even monoclinic.

Cheers
Roberto





On 5 Feb 2009, at 18:10, Francis E Reyes <[log in to unmask]>  
wrote:

> It seems like this space group will be the death of me.
>
> I'm working on a structure in SG P41212 one molecule per asu that was
> solved with experimental SAD phases.  The resolution is to 2.5 and the
> refinement is stuck at an R/Rfree of 30 and 33 with bonds rmsd of
> 0.011 and angles of 1.597 . The unit cell is 73.604   73.604  114.279
> 90.00  90.00  90.00.
>
> I'm considering the case of perfect twinning where the real s.g. is
> P41 masked under the higher symmetry in P41212.
>
> It seems to be the case in perfect twinning that the approach is to
> molecular replace the refined model into the lower space group. I
> reindexed my data to the lower space group P41 and molecular replaced
> into the reindexed data with Phaser. A single was solution was found
> with 2 mol per asu (39.6% solvent content) related by NCS.
> I've refined the now two fold ncs related structure in P41 to a much
> more respectable R/Rfree of 25.2 and 28.6 with rmsd bonds at 0.004 and
> angles at 0.865 refining with a twin law and NCS as implemented by
> phenix.refine.
>
> However I'm not happy:
> [1] a simmulated anneal omit map one of the monomers in P41 where 5
> residues in a non crystal contact region of the molecule (I wanted to
> challenge the omit map) shows nearly no density. (the SA OMIT map was
> generated with phenix.autobuild using the same refine parameters as
> the final round of refinement)
> [2] the NCS selection is a little bit troubling. (maybe the phenix
> developers can chime in on this)
>   reference = chain 'B' and (resseq 243:293 or resseq 310:370 )
>   selection = chain 'A' and (resseq 243:293 or resseq 310:370 )
> seems as if resseq 243:293 is behaving differently than 310:370?
> [3] the densities of the side chains of a helix (not an xtal contact)
> are poorly defined, with geometry for the backbone not so good.
>
>
> There's talk about choosing the correct MR solution (see On the
> molecular-replacement problem in the presence of merohedral twinning:
> structure of the N-terminal half-molecule of human lactoferrinW. A.
> Breyer, R. L. Kingston, B. F. Anderson and E. N. Baker ) . I use
> phaser to pick my MR solution for P41. Could phaser possibly have
> chosen poorly?
>
> Thanks!
>
> FR
>
>
> ---------------------------------------------
> Francis Reyes M.Sc.
> 215 UCB
> University of Colorado at Boulder
>
> gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D
>
> 8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

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