Dipankar,
An MR R-factor of 53% is close to what you get with a random, incorrect
solution. Even for challenging MR cases, your MR R-factor should
normally be under 50% before rigid-body refinement of the MR solution.
As others have mentioned, you should not proceed directly to refinement
unless you know your MR solution is sensible and you have fixed the
obvious problems otherwise you may lock in some model bias. There are a
few sanity checks you should perform before proceeding:
1. Inspect the model in Coot or Pymol (or whatever), turn on symmetry
molecules, and inspect molecule packing in the lattice. If you don't
get nicely packed molecules with reasonable intermolecular contacts
(no major clashes or interpenetrating molecules, no "lonely"
molecules) and obvious solvent channels, the space group is likely
wrong. Run Phaser with the option to look at all alternative space
groups.
2. Run a cell content analysis in Phaser. (You should do this first.)
This feature uses the Matthews probability calculator to estimate
the number of search models in the asymmetric unit. If you have too
many/too few models in the ASU, you won't get a good solution.
Inspecting packing of the lattice may alert you to having too
many/too few protein chains in the ASU.
3. Inspect your electron density maps. If it is difficult to trace the
main chain or see clear side chain density, it is not likely you
have a solution. However, some incorrect solutions can sometimes
give quasi-sensible-looking density. If your solution is decent, you
should be able to see non-protein features in the difference maps,
e.g. metal ions should stand out in metalloenzyme structures.
It is possible that your search model contains features (N- and
C-terminal secondary structures or loops) that are disordered in the
crystal. Including these in the search model can cause problems with
clashes and poor phasing. Again, inspecting the electron density and/or
clashes in the MR solution may alert you to this issue. Modifying your
search model appropriately may help. Or not.
If you have reason to believe your search model is a good one, Phaser or
Open-EPMR has never failed me, even with search models with just under
30% identity or high copy numbers per ASU.
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 3/14/2012 5:26 AM, Dipankar Manna wrote:
Dear Crystallographers,
Can anybody guide me how to reduce R-factor, means which are the basic
parameters I have to look for to reduce the R-factor during
refinement. I am newly learning the refinement. After running molrep
R-factor is around 53% (100% identity), after rigid body refinement
its showing around 49% and after restrained refinement its showing
around 47%. Highest resolution is 2.5A.
Regards
Dipankar
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