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
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