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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 <-- 26 March 2007Subject: Re: Solving a structure by MR with a pseudo-translation vector From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK Date: 2007-03-26 Remember you do not know your spacegroup. Absences along 0k0 and 00l will be very influenced by the translation. Sp you need to test all: P21 2 2 P21 21 2 P21 2 21 P21 21 21 Run MOLREP using the pseudo translation vector - it is an option in the GUI under search parameters. There wont be a clear distinction of course because they are all going to be almost equivalent but maybe there will be a marginal difference.. The features of the data you describe are the consequence of this translation.. Eleanor 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 > > > CCP4bb navigationCCP4bb <-- 2007 <-- March 2007 <-- 26 March 2007 |
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