Initially i will leave it untill i get reasonably good refinement stats.
More you refine these extra densities will clear up.You have a great resolution so
i would imagine you will see clear indications of chemical groups
If the ligand that you think is bound, is covalently linked or undergo any
reactions within the active site your density may not look like anything of your original ligand.
So i am just guessing here becoz details on your problem is very scanty.In that case you need
to know what are the possible reaction mechanism.
In any case you should suspect the obvious ones, that might interact
or any buffer molecules or any special detergents used in your protein preps or crystallization.
We see a lot of the extra denstiy comes from just the buffer molecules.
hope this helps.
Padayatti
On 11/8/06,
[EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
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Hello,
Does anybody have an idea how to identify a small molecule based on
density map? I have solved a structure at 1.7A and found a
mysterious fo-fc map at 3sigma. I believe it is the ligand
copurified with my protein. Is there a way to identify it in
addition to guess and try? I have done a lot of guessing and trying
without success.
Thanks.
Zhen
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Pius S Padayatti
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