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
