Dear Intekhab,
Before putting a lot of effort in trying to find the missing domain, you
first should make sure it is there. It may be that only two proteins of
the heterotrimer were packed in the crystal, or that one domain got
clipped off during crystallization. The way to do it, is to run an sds
page gel of a crystal, or a number of crystals if they are too small.
Best regards,
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of intekhab alam
Sent: Monday, August 22, 2011 9:12 AM
To: [email protected]
Subject: [ccp4bb] MR problem
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
