Dear Ed,
Thank you for the picture. The decarboxylation of GLU and ASP
side-chains is perhaps the most ubiquitous manifestation of radiation
damage. We have introduced a feature in our autoPROC processing
package whereby, if redundancy in the unmerged data is sufficient to
allow reasonably complete and non-overlapping "early" and "late"
data(sub)sets to be defined, we output "early-minus-late" difference
coefficients that can later be picked up by autoBUSTER to compute the
corresponding difference map. This is a great way of pin-pointing
acidic side-chains, and also sulphur-containing ones. I am sure others
are certain to propose a cooler name for that very same type of map
some day ;-) .
Here, you seem to have a clear case of partial decarboxylation.
You could try reprocessing your images with autoPROC and computing an
early-minus-late map, just to see what it looks like. If your dataset
complies with the modern low-transmission, high-redundancy paradigm,
it should be very straightforward. You are welcome to get in touch
off-list about this.
With best wishes,
Gerard.
--
On Wed, May 03, 2017 at 05:19:25PM -0400, Edward A. Berry wrote:
>
>
> On 05/03/2017 02:46 PM, Gerard Bricogne wrote:
> >Dear Ed,
> >
> > Have you considered the possibility that it could be a water
> >stepping in to fill the void created by partial decarboxylation of the
> >glutamate? That could be easily modelled, refined, and tested for its
> >ability to flatten the difference map.
> >
> > Gerard.
> >
> Actually some of them do appear decarboxylated. Is that something that can
> happen? In the crystal, or as radiation damage?
> However when there is density for the carboxylate (figure), it appears
> continuous and linear, doesn't break up into spheres at H-bonding distance -
> almost like the CO2 is still sitting there- but I guess it would get hydrated
> to bicarbonate. I could use azide. Or maybe waters with some disorder.
> Thanks,
> eab
>
> Figure- 2mFo-DFc at 1.3 sigma, mFo-DFc at 3 sigma, green CO2 is shown for
> comparison, not part of the model.
>
