Dear Appu,
you give very little details, so it is not possible to give very
specific advice. Here are some general points:
-the Mw of your protein is 36 kDa, what is the Mw of the ligand binding
domain and of the DNA binding domain? If the ligand binding domain is a
seizable part of the total, you may get enough phase information from
the ligand binding domain alone. This will depend on the resolution you
have. Did you have a look at the electron density maps, phased with the
ligand binding domain alone?
-I asume you used the DNA- and ligand binding domains as separate models
and not the full-length protein? If not, you should separate the domains
and remove the linker from your search model and run again molecular
replacement.
-Are there different models for the DNA binding domain available (from
other complexes, homologous proteins)? If so, you should try these as
well, or even try them all at once. How this is done is explained in the
phaser manual.
-The most probable Mw in the asu is the Mw which would give ~50%
solvent. If your Mw is different, this means that you either have a lot
of solvent (1 molecule in the asu) or little solvent (2 molecules in the
asu). You have to try both options.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Appu kumar
Sent: Monday, February 18, 2013 10:52 AM
To: [email protected]
Subject: [ccp4bb] molecular replacement for flexible domain of
protein
Dear ccp4 user,
I have problem in finding the phase for
the flexible DNA binding domain of LTTR protein. The unit cell
parameters are ,Unit Cell: 46.92 105.30 47.75 90.00 103.26 90.00, and
space-Group P 1 21 1. Molecular weight of protein is 36000Da. When i am
running phaser it showing that
Most probable MW of protein in asu for resolution = 49714.8.
Could you please guide me how to set the proper setting for finding the
correct rotation function and translation function setting to get the
phases for the full length protein. I m getting the phases for the
ligand binding domain but not for the DNA binding domain. Could you
please suggest me some tricks which would work to get the phase. Thanks
a lot in advance
Appu
