Re: [ccp4bb]: Problems with C2 (fwd)

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

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Daan van Aalten wrote:
> 
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> 
> Hi All
> 
> We are experiencing some weird problems with MR and subsequent building
> in C2. MR (with different programs) gives clear solutions (R~45%,
> CC~35%) that make good sense from packing considerations. Since we have
> high resolution data (1.9 A for apo, 0.95 A for complex) we feed this
> straight into warpNtrace which builds only about 15% of the structure with
> some good looking secondary structure elements. Further refinement, or
> refinement starting straight from the MR solutions halts with R-factors >
> 40%.
> 
> Some vital stats:
> 
> - UNIT CELL
> 
>     85.533 34.317 43.796 90.000 112.664 90.000 c2
> 


 I dont think this can be twinned - you need some way of relating a*, c*
and/ a*-c* , a*+c* etc.. so their cell dimensions have to correspond
quite exactly.

 Axis search gives these possible axis lengths:
  10 shortest spacing in reciprocal lattice

 Reciprocal lattice vector and Length:   1   0   0  0.012670
 Reciprocal lattice vector and Length:   1   0  -1  0.023047
 Reciprocal lattice vector and Length:   0   0   1  0.024744
 Reciprocal lattice vector and Length:   2   0   0  0.025339
 Reciprocal lattice vector and Length:   2   0  -1  0.027770
 Reciprocal lattice vector and Length:   0   1   0  0.029140
 Reciprocal lattice vector and Length:   1  -1   0  0.031775
 Reciprocal lattice vector and Length:   1   1   0  0.031775
 Reciprocal lattice vector and Length:   1   0   1  0.031849
 Reciprocal lattice vector and Length:   3   0  -1  0.036499


 I dont think 1 0 -1 at 0.0230 and 2 0 0 at 0.0247 are close enough..

 Have you looked at the 2nd moment plots from truncate and the native 4A
patterson to see if the 2nd moments look non standard, or if there is
pseudo NCS translation..

  Do you mean really 0.95A data for complex? If so the phases can easily
be improved with ACORN from the MR starting point, In our experience
this makes it very easy for Arp/Warp.

 Eleanor


> 
> The CCP4 Twinning page suggests twinning in C2 can be solved by
> re-indexing the data with different unit cell settings, but it's not clear
> how this should be done.
> 
> Thanks in advance for any help!
> 
> cheers
> 
> Daan
> 
> ##############################################################################
> 
> Dr. Daan van Aalten                    Wellcome Trust RCD Fellow
> Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
> Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
> School of Life Sciences                E-mail: dava@davapc1.bioch.dundee.ac.uk
> Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk
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