Le Jeudi 4 Mai 2017 12:25 CEST, Andrew Leslie <and...@mrc-lmb.cam.ac.uk> a écrit:
Dear Andrew, We looked in details to this problem of diffusion at ca. 100 K with bromine in "Ennifar et al., Acta D58(2002)1262" and we concluded "It was attempted to derive a value for the diffusion coefficient of the free bromine species (most likely Br-) in amorphous ice at 100±110 K. This failed because the diffusion was much too rapid compared with both the radiolysis and datacollection timescales to permit such a determination." Best regards Philippe Dumas > 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>
