At 2A I think you will see the difference between the 2A bond Mg-GLU and
the likely 2.8A HOH-GLU.
Look at your difference map - put a peak there and check distances to
surrounding atoms.
Marjorie Hardings metal protein server gives a guide to other putative
Mg binding.
Eleanor
On 12/15/2011 08:10 AM, Phil Evans wrote:
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
