This seems to be very a common scenario in MR and recently we have added
some code to phaser.MRage that would handle it automatically. Each partial
solution is analysed for the presence of (complete of incomplete)
assemblies that obey local point group symmetry. After such an assembly is
identified, the program can either "fill in" molecules where they should be
(provided the obey the previously identified local symmetry), and can also
search with the full assembly. This greatly enhances the signal (since the
model comprises a larger fraction of the asymmetric unit), and also speeds
up the search.
(MRage is not yet included in the current CCP4 release, but available as
alpha-test in recent Phenix nightly builds.)
BW, Gabor
On Apr 30 2012, Roger Rowlett wrote:
A partial solution can potentially lead you to an appropriate MR
solution. With many protein chains in the ASU, there will be several
"reasonable" possibilities by Matthews analysis. When I originally
solved 2A8D, cell content analysis suggested 8 monomers per ASU, but it
was clear after a few MR runs that was not going to work. Inspecting the
packing of a partial solution with 4 monomers, which formed a nice,
biological-looking tetramer, clearly suggested that another dimer would
fit into the lattice just nicely. A search with 3 such dimers produced
an excellent MR solution starting point for the final refinement. I used
a similar procedure for 3UAO. The Matthews analysis suggested 10-12
chains per ASU, but it was clearly 8 based on packing of partial
solutions. A 4-dimer search was immediately successful.
Cheers,
_______________________________________
Roger S. Rowlett
Gordon & Dorothy Kline Professor
Department of Chemistry
Colgate University
13 Oak Drive
Hamilton, NY 13346
tel: (315)-228-7245
ofc: (315)-228-7395
fax: (315)-228-7935
email: rrowl...@colgate.edu
On 4/30/2012 5:20 PM, mjvdwo...@netscape.net wrote:
Provided that you guess the number of copies and your guess is
reasonably close, my experience is that Phaser will do the job. But
you have to tell it how many copies you expect, or it will never make
sense of the data. When I did my structure with 6(?) copies some years
ago, I guessed a number that was close enough and then when I
inspected the electron density I could see that there were more copies
than I had told the software and all was fine after that. It was
surprising to see that good solutions were obvious from a packing
consideration, while inadequate solutions were obviously wrong.
Mark
-----Original Message-----
From: Ke, Jiyuan <jiyuan...@vai.org>
To: CCP4BB <CCP4BB@JISCMAIL.AC.UK>
Sent: Mon, Apr 30, 2012 2:28 pm
Subject: [ccp4bb] Suggestions for solving a structure with 8-10 copies
per asymmetric unit
Dear All, I have a question regarding solving a crystal structure by
molecular replacement. It is a single protein with a molecular weight of
25.5 kDa. The cell dimension is rather big from the diffraction data (
90.9 Å, 143.9 Å, 216.3Å, 90°, 90°, 90°). The possible space group is
P212121. With such a big unit cell, we predicted that there are 8-10
molecules per asymmetric unit. We have a decent model with sequence
similarity of 49%. I tried several times with Phaser search with the
current model and had difficulty to find any clear solution. Has anyone
seen such cases and any suggestions to solve the structure? Thanks!
Jiyuan Ke, Ph.D. Research Scientist Van Andel Research Institute 333
Bostwick Ave NE Grand Rapids, MI 49503
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Cambridge Institute for Medical Research
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