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Re: [ccp4bb] Solving a structure by MR with a pseudo-translation vector |
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CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 24 March 2007Subject: 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 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 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 navigationCCP4bb <-- 2007 <-- March 2007 <-- 24 March 2007 |
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