Thank you all for the help. These are the key factors I collected so far: 1. Distance, Mg--O is shorter (2.0 -- 2.4A) 2. Coordination, Mg is octahedrally coordinated. 3. B factors, local B factors (i.e. the residues that coordinate with the ion) should be similar. 4. Use Mn++ to replace Mg. I will look into these more.
Best, Gao On Wed, Dec 14, 2011 at 5:45 PM, bie gao <[email protected]> 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 >
