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Hi Folks:
First of all, many thanks to those who responded to my first email.
I apologize for it being so unclear. I now have a much clearer idea
of the problem, so let me start again:
I'm refining a previously solved RNA structure in which we have
soaked 10 mM Mg++ and collected data near the absorption edge.
I identified the sites with an anomalous difference Fourier and the
strongest Mn++ peak is one in which GDP at the 5' end of my RNA binds
Mn++ via N7 and the beta phosphate in a completely chemically
reasonable way. Adding the Mn++ made the refinement behave funny. I
since found out we also have a remote data set on the same crystal,
so once I used that, things started behaving much better. The most
striking difference is in the 2Fo - Fc maps.
http://www.chemistry.ucsc.edu/~wgscott/temp/weirdmaps.pdf
The above link is to a pdf that shows the Mn2+ at the inflection is
quite weak, despite using the model with Mn2+ bound. The same model,
after one cycle of refinement in refmac after switching to the remote
data, is much more normal. The density at the same Mn++ site is
stronger than the adjacent phosphori density.
So for whatever reason, refmac (or, more likely, the idiot running
it) isn't modeling the real part of the dispersive term correctly,
but the problem seems to go away when I am not at the dispersion
maximum (the absorbance inflection point).
Anyway, the simple answer to my question is to use the remote data
for refinement, but had we not collected multiple wavelength data
sets on this metal soak, is there a way that I could more reliably
model the Mn++ scattering at the inflection point?
Thanks.
Bill
