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
