>Dear all,
>    We are working on protein-inhibitor complex crystal structures, although 
> we did get nice crystals and soaked them with >inhibitor for several days, 
> all structures we obtained were empty!!There are nothing at the active site. 
> For several crystals. >their color turned very clearly from colorless to 
> yellow the color of the inhibitors, nothing found either.

Perhaps attempt growing the crystals in the presence of the inhibitor instead 
of soaking. 

>    These inhibitors work very well in enzyme assay. We, especially our 
> students, are very depressed...
>    Any suggestions will be really appreciated!

A fascinating component of science is exploring issues that do not follow our 
preconceived notions.  Nature it seems doesn't have much sympathy for how we 
feel so may as well keep your head up.

All the Best,

Sean

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