Dear 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 higher
than that of normal cases. More details about solving incommensurately
modulated structures can be found on the Webpage:

http://cryst.iphy.ac.cn <http://cryst.iphy.ac.cn/> 

 

Hai-fu

 

--

Professor Fan, Hai-fu

Institute of Physics

Chinese Academy of Sciences

Beijing 100080, P.R. China

 

Email: [EMAIL PROTECTED]

URL: http://cryst.iphy.ac.cn <http://cryst.iphy.ac.cn/> 

 

 

-----Original Message-----
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Peter
J Stogios
Sent: 2007年3月25日 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, 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

 

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