Molecular replacement in real space

["chunmin li" <chunmin@shomer.BIOC.CWRU.Edu>]

***  For details on how to be removed from this list visit the  ***
***    CCP4 home page http://www.dl.ac.uk/CCP/CCP4/main.html    ***

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).  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?

Tnanks in advance!


Chunmin Li

-- 
************************************
chunmin li
Case Western Reserve University
School of Medicine
Department of Biochemistry
10900 Euclid Ave
Cleveland, Ohio 44106-4935

chunmin@shomer.bioc.cwru.edu
************************************