Re: Molecular replacement in real space

[Eleanor Dodson <ccp4@yorvic.york.ac.uk>]

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On Jul 30,  7:44pm, chunmin li wrote:
> Subject: Molecular replacement in real space
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> Hi, there,
>
> We are now trying to solve a protein-inhibitor complex structure by combining
> both MR and MIR methods.  Although we have several heavy atom derivatives,
only
> one of them is relatively good.  Therefore we can not trace the chain on the
> MIR map.  We know the crystal structure of the inhibitor, which is one
seventh
> of the protein-inhibitor complex.  What we are doing now is searching
> this inhibitor on the MIR map using AmoRe (molecular replacement in real
> space).


>
> There are four molecules in the a. u.  From the results of self-rotation
> function calculation we know the four monomers in the a. u. are related by
> 222 symmetry.  Now four solutions of the rotation search satisfy the
> 222 symmetry.  The top solutions of translation search using them do not
> seem right (we looked the packing of the generated tetramer).


 But a generated tetramer of 4* 1/7 of the complex? Do you expect all the
inhibitors to fit together? Maybe it is the big protein which forms the
tetramer? with 4 little inhibitors on the edges?
> It is possible
> that the four solutions of the rotation search are wrong.  I am just
wondering
> that in the case that the four solutions of the rotation search are right,
> and translation solutions are buried in many possible solutions, is there a
> easy way to recognize the right translation solutions since we know the space
> group of the crystals and the heavy atom positions?  Is there any suggestion
> how to do molecular replacement using only a small part of the protein
> structure?
>


 I think it might be sensible to try a phased translation search with the
various rotation fn solutions..
 Or just look at where they sit in the SIR map..

 Eleanor Dodson

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Eleanor J.Dodson, Chemistry Department, University of York, U.K.
Tel: Home +44 (1904) 42 44 49, work:  +44 (1904) 43 25 65
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