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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