[ccp4bb] Solving a structure by MR with a pseudo-translation vector

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-03-24

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Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: Esko Oksanen esko {- dot -} oksanen {- at -} HELSINKI {- dot -} FI
Date: 2007-03-24

Subject: Solving a structure by MR with a pseudo-translation vector
From: Peter J Stogios pstogios {- at -} UHNRES {- dot -} UTORONTO {- dot -} CA
Date: 2007-03-24

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: pstogios@uhnres.utoronto.ca
w: http://xtal.uhnres.utoronto.ca/prive
p: (416) 581-7543

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Expression hosts (was:Inclusion body)
From: Artem Evdokimov artem {- at -} XTALS {- dot -} ORG
Date: 2007-03-24

Next message:
Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: Esko Oksanen esko {- dot -} oksanen {- at -} HELSINKI {- dot -} FI
Date: 2007-03-24