Dear Dhanasekaran,
There are many examples of molecular replacement failing even in cases
where the model and target structure share 100% sequence identity. These
examples illuminate several factors that MR search strategies are sensitive
to, including percent sequence identity and related parameters like RMSD
from target, the impact of loops, small domain movements etc.
So if you want to learn in more depth about what makes a good model and
what makes or breaks an MR search, perhaps some googling combined with a
bit of obsessive reading might help. I actually found a ton of thoroughly
helpful articles and reviews for MR on the web without too much sweat.
Best wishes,
Raji
On Thu, Sep 12, 2013 at 5:21 PM, Dhanasekaran Varudharasu
dhana...@gmail.com wrote:
Dear crystallographers,
I have solved a structure of a glucose
binding protein of CE4 family. When I try to solve the structure using the
same CE4 family enzyme as search model, it failed for many case. Finally, I
solved the with a same family enzyme used as search model. As soon as I
solved the structure, I superposed my final refined model with structures
of CE4 family enzymes which did not produce the good molecular replacement
solution for my enzyme. I found that all are having (Beta/alpha)7 fold and
superpose very well with my model. Whereas, some loop region are not
superpose very well. My doubt is why molecular replacement failed thought
over-all fold is same?.
--
*Dhanasekaran Varudharasu*
Post-Doctoral Fellow
Department of Oral Biology
Rutgers school of Dental Medicine
Rutgers Biomedical and Health Sciences
Newark, NJ 07103
USA
--
Raji Edayathumangalam
Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University