I doubt that you can tell the difference between Mg and water just from the height of the density, but Mg2+ is always octahedrally coordinated with Mg-O bond lengths ~2.0A At 2.9A resolution you may not be able to distinguish
Phil
On 14 Dec 2011, at 22:45, bie gao wrote:
> Hi every,
>
> I'm working with 2 crystal forms of a protein from 2 different crystallization conditions. Condition 1 has 100mM MgCl2. Condition 2 doesn't. Both are ~2.9 angstrom. The 2 structures are virtually identical except in condition1, there is a clear positive density surrounded by a Glu side chain carboxyl and a couple of main carboxyl groups. (Again, condition 2 doesn't have this density).
>
> My initial thought is that a Mg atom is incorporated and it fits well. But the problem is we can not role out the possibility of a water molecule. Refining with Mg gives a b-factor of 42 (about average for the whole protein). The b-factor is 21 when refining with a water. Both cases there is no positive/negative density at contour=2.0.
>
> Based on the current data, is there any other role we can apply to see how likely it is a Mg or water. Or anomalous scattering is the only way? Thanks for your suggestions.
>
> Best,
> Gao
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