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

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

Previous 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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Subject: Re: Solving a structure by MR with a pseudo-translation vector
From: Petrus H Zwart PHZwart {- at -} LBL {- dot -} GOV
Date: 2007-03-25

Dear Prof. Fan,
I do not think that this is a neccesarely an incommensurable structure. A lot of structures have translational NCS close to a translational that would make the space group higher and/or the primitive cell smaller.
If one has C2221 and one destroys the centring operation x,y+1/2,z+1/2 by introducing a small perturbation, one just has pseudo symmetry/pseudo centring.
If the data is processed in P212121, there need not be satelite reflections. If one wrongly assumes the sg to be C2221, there are 'satelite' reflections: the systematic absences due to the imperfect lattice translation (x,y+1/2,z+1/2).
HTH
Peter

> It seems to me that you are solving an incommensurately modulated
> structure,since the pseudo-translation vector t = 0a + 0.47b +
> 0.5c having the b
> component equal to 0.47 and not exactly 0.5. There should be satellite
> reflections which are NOT on nodes of the reciprocal lattice you have
> chosen. If you try to solve an incommensurately modulated
> structure by
> rejecting satellites, what you get will be the ¡°averaged
> structure¡± and
> not the true structure. In this case R factors should considerably
> higherthan that of normal cases. More details about solving
> incommensuratelymodulated structures can be found on the Webpage:
>
> http://cryst.iphy.ac.cn
>
>
>
> Hai-fu
>
>
>
> --
>
> Professor Fan, Hai-fu
>
> Institute of Physics
>
> Chinese Academy of Sciences
>
> Beijing 100080, P.R. China
>
>
>
> Email: fanhf@cryst.iphy.ac.cn
>
> URL: http://cryst.iphy.ac.cn
>
>
>
>
>
> -----Original Message-----
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
> Of Peter
> J Stogios
> Sent: 2007Äê3ÔÂ25ÈÕ 4:52
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Solving a structure by MR with a pseudo-
> translation vector
>
>
>
> 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, Priv¨¦ 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: 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

Next message:
Subject: Re: Nature policy update regarding source code
From: Nat Echols echols {- at -} UCLINK {- dot -} BERKELEY {- dot -} EDU
Date: 2007-03-25