As already noted, it is possible that the other domain is not present,
or not ordered. Try refining a bit without it, and see what your stats
look like.
It is also possible that it is present, but minor clashes are causing
good solutions to be rejected. Go into the output file and examine the
TF scores before overlap rejection.
The R and Rfree sound pretty good for an MR solution. About the failure
of these numbers to come down, I'm not sure what you tried. Refinement
with REFMAC5 should bring them down. You should see indications in the
2fo-fc and fo-fc maps that they are accurate - i.e. that there are real
features showing up that are not in your model. You can test that also
by deleting some prominent side chains.
On 08/22/11 03:12, intekhab alam wrote:
Hi there
I have a data of heterotrimer protein complex at 2.9A resolution.
One protein consists of two domains. I tried phaser as well as molrep
which gives a solution with only one domain.
Rotation function and translation function were found to be fine for
these solutions.
I tried to find missing domain of the protein after fixing one of the
domain or the other partner proteins using whole part or various
truncations of missing domain.
I also tried to find and build missing domain using Rosetta with the
solutions of Molrep or Phaser as template.
But, there were no solutions, or the solutions are clashed with other
domain or proteins.
Furthermore, R and Rfree is 30 and 40, respectively, and I could not
reduce them further.
There was almost no electron density map in the empty space so that I
could not model manually.
Plz guide me ,how can i look for the missing domain in the protein.
regards
--
INTEKHAB ALAM
LABORATORY OF STRUCTURAL BIOINFORMATICS
KOREA UNIVERSITY, SEOUL
--
=======================================================================
All Things Serve the Beam
=======================================================================
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[email protected]
