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

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CCP4bb <-- 2007 <-- March 2007 <-- 24 March 2007
Previous message:
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 		Next message:
Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-03-24


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
Peter,

I had a similar case, but the centering was pseudo-I in the
monoclinic system (Oksanen et al. (2006) Acta Cryst. D62 1369-1374).
I don't think you need to delete any reflections for MR; you should
have higher than normal correlation coefficients as well as R-values.
If you see the pseudo-translation vector between the two molecules,
the solution is probably the correct one. The problem is that when
you scale your data, the error model assumes a different intensity
distribution than what you actually have. Therefore your weak
reflections will have very high sigmas and since they define the
_position_ of the molecules in the ASU, you are refining essentially
against zeros in rigid body refinement. What I did was to scale the
odd and even reflections separately, and then do rigid body
refinement against the odd (weak) and restrained refinement against
the even (strong) reflections. In the presence of significant pseudo-
symmetry, the structure is probably never going to refine very well,
at least in terms of R-value, because it is no longer a very good
indicator of structure correctness...

HTH,
Esko

Esko Oksanen, M.Sc., researcher
Macromolecular Structures Group
Research Program in Structural Biology and Biophysics
Institute of Biotechnology, University of Helsinki
Viikinkaari 1 P.O. Box 65
FIN-00014 Helsinki
FINLAND
tel. +358-9-19158953 fax +358-9-19159940
mob. +358-50-3771414
Skype ejoksane
esko.oksanen@helsinki.fi


On Mar 24, 2007, at 21:51, 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: pstogios@uhnres.utoronto.ca
> w: http://xtal.uhnres.utoronto.ca/prive
> p: (416) 581-7543


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CCP4bb <-- 2007 <-- March 2007 <-- 24 March 2007
Previous message:
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 		Next message:
Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: "Fan, Hai-fu" fanhf {- at -} CRYST {- dot -} IPHY {- dot -} AC {- dot -} CN
Date: 2007-03-24


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