Re: [ccp4bb]: Ions in the internal protein cavities - addendum

[Bart Hazes <bhazes@ualberta.ca>]

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You never say what your crystallisation conditions are. From the description
it sounds like your density is a single-atom, or atom + hydrogens, positively
charged ion. Ammonium, sodium, potassium spring to mind, especially if any of
these were in the mother liquor. The coordination or hydrogen bonding may not
be exactly what you expect for these groups but the enviroment of a
hydrophobically shielded cluster of 3 negative charges may just want to pull
in some counterion. It will be hard to prove unambiguously what it is.
However, if you use any of these monovalent ions as an additive or precipitant
you could try to switch to another similar but heavier or lighter element and
see if the peak gets stronger or weaker.

Bart


On Thu, 31 May 2001, Petr Leiman wrote:

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> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> >Because the piece is surrounded by the hydrophobics I
> >think that the material of the piece is there from the moment when the
> >protein get folded and this material did not come from the purification
>
> >or crystallization solutions.
>
> The Asps and the piece in between them form a plane, which is surrounded
> by hydrophobics from all sides. It would be stupid to say that an Aps is
> hydrophobic.
>
> Petr
>

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