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CCP4BB  March 2007

CCP4BB March 2007

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Subject:

Re: Solving a structure by MR with a pseudo-translation vector

From:

Eleanor Dodson <[log in to unmask]>

Reply-To:

[log in to unmask][log in to unmask], 14 Mar 2007 10:45:48 +0000337_ISO-8859-1 Here's an updated version of cns2mtz. The new version automatically
merges anomalous data, generates a full set of CCP4-style free sets from
the CNS test column, completes the data (unless you tell it not to), and
can take the cell and spacegroup information from a pdb file as well
as from the command line. [...]44_14Mar200710:45:[log in to unmask]

Date:

Mon, 26 Mar 2007 11:58:45 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (80 lines)

These structures are horrible..
  Remember you do not know your spacegroup.
Absences along 0k0 and 00l will be very influenced by the translation.

 Sp you need to test all: P21 2 2 P21 21 2    P21 2 21     P21 21 21
Run MOLREP using the pseudo translation vector - it is an option in the 
GUI  under search parameters.

There wont be a clear distinction of course because they are all going 
to be almost equivalent but maybe there will be a marginal  difference..

The features of the data you describe are the consequence of this 
translation..
Eleanor




Peter J Stogios wrote:
> Hello,
>
> I posted a message about this a month ago and thanks to everyone for 
> their responses.  At the time, I did not fully appreciate the problem 
> I was dealing with so this time my question is much more specific.  I 
> would very much appreciate your help as this structure is turning out 
> to be very difficult to solve!
>
> I am trying to solve a structure by MR that should be easy, given that 
> I have solved multiple structures of homologous proteins by the same 
> means.  This crystal is 2.6 angstrom, apparently P212121, with two 
> molecules in the asymmetric unit that are related by the 
> pseudo-translation vector (0, 0.47, 0.5).  This vector was identified 
> from the Patterson map, it is a peak 45% the height of the origin peak.
>
> As well, I have looked at all the reflection parity groups.  Based on 
> I/sigmaI values output by Truncate, the k+l = 2n reflections are as 
> high as 2-fold greater in I/sigI vs. k+l = 2n+1 reflections from 16 to 
> 5.1 angstrom.  From 5.1 to 2.9 angstrom, the reverse is true: the k+l 
> = 2n reflections are as high as 0.62-fold LOWER in I/sigI vs. k+l = 
> 2n+1.  Then, from 2.9 to 2.6 angstrom, each reflection class is 
> approximately equal in intensity.
>
> MR using Molrep's multi-copy search, using all reflections, 
> consistently reproduces the pseudo-translation vector as the dyad 
> vector between the two molecules.  However, these solutions are not 
> easily noticeable (Molrep just picks the highest score but this score 
> does not stick out from the pack), and these solutions do not refine 
> well via rigid body or restrained refinement in Refmac.
>
> I have found some papers that show successful structure determinations 
> by MR with pseudo-translation, but I am not sure which approach to 
> take to solve my structure.  Do I need to remove the pseudo-weak or 
> pseudo-strong reflections?  Or do I actually use the pseudo-weak or 
> pseudo-strong reflections for the MR since they will contain the 
> information from the pseudo-translation?  Which reflections should I 
> refine against?  Should I reindex to C222 to reflect the pseudo-face 
> centering from the (0, 0.47, 0.5) vector?  Or am I missing something 
> completely?
>
> Any help would be very very much appreciated!!!!  Thanks!
>
>
> Peter
>
>
> ~
> Peter J Stogios
> Ph.D. candidate, Privé Lab
> Dept. of Medical Biophysics, University of Toronto
> Toronto Medical Discoveries Tower (TMDT) at MaRS
> 101 College St., Rm. 4-308
> Toronto, Ontario M5G 1L7
>
> e: [log in to unmask]
> w: http://xtal.uhnres.utoronto.ca/prive
> p: (416) 581-7543
>
>
>

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