Dear Ed,
I find your electron density quite interesting, because generally
(I think, I would be happy to be corrected on this) when de-carboxylation of
Asp/Glu occurs due to radiation damage, there is no evidence of what happens to
the resulting CO2 group. One interpretation of this is that it diffuses away
from the side chain and is effectively totally disordered, so no electron
density is seen, but I was surprised that this would always be the case,
especially as I would have thought that diffusion would be quite limited at
100K (maybe I’m wrong about that too, but that is supposed to be one reason why
radiation damage is less at 100K).
If the residual density is due to partial de-carboxylation, then I would have
expected density for the CG-CD bond, which is not present (at your chosen
contour level).
Do many of your Glu side chains have the residual density?
Best wishes,
Andrew
> On 3 May 2017, at 22:19, Edward A. Berry <ber...@upstate.edu> 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.
>
> <decarbox.gif>
