[phenixbb] following on the anomalous map

Nathaniel Echols nechols at lbl.gov
Tue Aug 26 08:48:42 PDT 2014

On Tue, Aug 26, 2014 at 6:49 AM, CPMAS Chen <cpmasmit at gmail.com> wrote:

> Since I have some MET and CYT in the protein, could I try to supply their
> sulfur as the initial anomalous scatters?

Technically this would work, but I don't see much point.  At the Br
absorption peak you'd expect an f'' of at least 3.8e- for Br, versus 0.2e-
for the sulfurs, which means that Br should be by far the largest peak in
the map unless it's just not there at all.  Refining anomalous scattering
the sulfurs won't change this.  (What the LLG map is useful for is the
reverse - refine the anomalous scattering for Br, and the LLG map will more
clearly show the sulfurs.)

As for the anomalous isomorphous difference map, would it be useful I
> compare the datasets acquired at 1A wavelength and at the Br absorption
> peak (~0.92A)?

Yes, the anomalous 0.92Å-minus-1.0Å map would be expected to show a
positive peak around any Br atoms (it works for SeMet MAD data, at least).
 But again, I think if it is bound at all the conventional anomalous
difference map for the 0.92Å data should be clear enough if the ligand is
bound at high enough occupancy to be modeled accurately.

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