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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:
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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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