Negative (or positive) density tells you what you that what you've
modelled is wrong.
If you have 1.15A X-ray data and it's telling you what you think is Ca2+
is not Ca2+, then I would think your X-ray data wins and your previous
structures lose (a lot can happen from one structure to the next...). I
must say, your 2fo-fc looks like a perfectly good Mg2+, since it is the
same size (ish) as the surrounding O and C atoms; a Ca2+ would have
given a much larger green blob.
phx.
On 30/06/2010 02:35, xaravich ivan wrote:
> Dear CCP4BB,
>
> I have come across something that might be pretty obvious to
> experienced people but is making me crazy.
> I have this great 1.15 angs data and I know that I have a Calcium ion
> (pics attached) from previous structures of the same protein, that I
> have solved. Rightly when I add waters with Arp solvent it does not
> put water at that positive density.
> Now whenever I have tried to put the calcium, and refine the structure
> it is giving me a negative density at the metal site. I csn see that
> the 2fc-fo is clear there, but why negative density. This is just the
> start of my refinement and I have to refine multiple ligands in the
> structure and I would like to get past this issue before that.
>
> I tried putting atom at the pointer, adding water and renaming it
> according to the naming convention in the PDB for Calcium, but nothing.
>
> Your suggestions would be invaluable, as always.
>
> Ivan
>
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