Hmm... this is a bit of a philosophical pickle in my mind.
I agree.
Right now I want as accurate a model as possible to improve the phases for
interpretation of a few remaining bits. I haven't decided what to deposit-
maybe three separate structures:
1. Conservatively modeled: Everything that I can't model is left unmodelled.
2. Speculative: every little green blob is filled with partial-occupancy water,
methanol, ethanol, acetate/bicarbonate, isopropanol, glycerol, Tris, or PEG
fragments. If peroxy-glutamate fits better, put it.
3. repaired model- rebuild the damaged glutamates, cycteines and methionines. Average the two
heterotetramers in the asymmetric unit to make one BioMolecule, and do a few ps of molecular
dynamics to eliminate crystallization artifacts. (Since this would now be a "solution
structure" I wouldn't be expected to report R-factor or deposit diffraction data for this
one). More likely it would be rejected as a "Model".
eab
On 05/09/2017 11:45 AM, Tristan Croll wrote:
Hmm... this is a bit of a philosophical pickle in my mind. Do we want to model
the structure as what it looks like after radiation damage has had its way with
it, or what it must have looked like *before* the damage? I can see arguments
both ways (and can sympathise with the former if you want to make radiation
damage a subject of your manuscript), but this is going to lead to headaches
for people who want to make use of the resulting coordinates to study the
actual biology of your protein. Personally, I'd strongly prefer the latter
approach.
Tristan
On 2017-05-09 16:06, Edward A. Berry wrote:
On 05/09/2017 06:18 AM, Ian Tickle wrote:
We have seen almost identical density to Ed's for GLU side-chains, with what looks like a linear molecule (yes
exactly the size of CO2!) where the carboxylate group would be and absolutely no density for the CG-CD bond. So
it's indeed very tempting to say that the CO2 is still there, and presumably making the same H bonds that the
carboxylate was making to hold it there. It would not be hydrated to carbonic acid, according to
https://en.wikipedia.org/wiki/Carbonic_acid : "The hydration <https://en.wikipedia.org/wiki/Hydrate>
equilibrium constant <https://en.wikipedia.org/wiki/Equilibrium_constant> at 25 °C is called K_h , which in
the case of carbonic acid is [H_2 CO_3 ]/[CO_2 ] ≈ 1.7×10^−3 in pure water^[5]
<https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-HS-5> and ≈ 1.2×10^−3 in seawater
<https://en.wikipedia.org/wiki/Seawater>.^[6]
<https://en.wikipedia.org/wiki/Carbonic_acid#cite_note-SB-6> Hence, the majority of the carbon dioxide is
not converted into car
b
o
n
ic
acid, remaining as CO_2 molecules.".
It looks like this ignores subsequent ionization of H2CO3 which would
be quite spontaneous at neutral pH. However the Wikipedia article
also indicates the equilibrium is quite slow (which makes sense-
otherwise why would carbonic anhydrase exist?) and it would be a great
deal slower in vitreous ice at 100 K. Anyway, I had reached the same
conclusion and have modeled a number of the troublesome glutamates as
decarboxylated with CO2 hovering above. There is a problem that the
remaining CG tends to push the CO2 a little out of the density in some
cases, but not a severe clash and it may work itself out with further
refinement or manual assistance.
eab
