Perhaps some "correct" solutions were thrown out due to packing
considerations.
There are a few methods to address that possibility. You could use a
search model with large loops trimmed, especially is a sequence
comparison shows they are probably not conserved. Or you could search
with a suite of structures from the family.
On 09/12/13 17:21, Dhanasekaran Varudharasu 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
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All Things Serve the Beam
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David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu