Dear Bie Gao, You can obtain an estimate of the standard deviation on your putative Mg to ligand distance using the diffraction precision index (DPI) approach of Cruickshank and Blow (1999 and 2002 Acta Cryst D). ie:- D M Blow Acta Cryst. (2002). D58, 792-797 Synopsis: The formulae for the diffraction-component precision index introduced by Cruickshank [(1999), Acta Cryst. D55, 583-601] are simplifed using two approximations. A rearranged formula for the precision index is presented which can readily be calculated from experimental data.
Using this you can add a quantitative test of statistical significance to the, of course, very senible earlier inputs to your questions. Do note though that the DPI is calculated as a number for the position error, sigma (x), on an atom with an average B factor. You have to adjust your DPI value for the atoms in question via the square root of their B value ratioed to the average B. For example a lower than average B gives a more precise sigma (x) than the average. Finally the sigma on the bond distance itself is calculated from the sigma (x) pair of values for each atom via the quadrature formula. The usual statistical test of significance is if the ligand distance (L) is then >3sigma (L). Best wishes, Prof John R Helliwell DSc. On Thu, Dec 15, 2011 at 9:29 PM, bie gao <gao...@gmail.com> wrote: > 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 <gao...@gmail.com> 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 > > -- Professor John R Helliwell DSc
