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: [EMAIL PROTECTED]
w: http://xtal.uhnres.utoronto.ca/prive
p: (416) 581-7543
