I have seen anomalous "flecks" bespangling an protein's internal cavity which had a couple of cysteines in it, and I assumed that these were liberated sulphurs (they were not Fourier-truncation-like.) I would agree with Andrew that diffusion should not be large, but alighting on the nearest perch should be possible, no? Attractive and repulsive forces remain just as strong at 100K, so although motions are not driven by thermal sampling or random-walking, they would still be driven by local forces.
Further, I would think that the likeliest local perches would appear as new sites, for the CO2 as well as for sulphurs. JPK -----Original Message----- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of DUMAS Philippe (VIE) Sent: Thursday, May 04, 2017 6:57 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] peroxy-glutamate? 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>
