Thanks all,
the pH is 6.7, azide is 3 mM, and there is no added ammonium.
I could get away with modeling as two waters since the separation is well above
the 2.2A that gets flagged as a clash in the PDB, still it's close enough
to suggest that two waters is not really what's there.
Enrico Stura wrote:
> Dear CCP4BB,
>
> The most likely components are those at the highest concentration in the crystallization
> or cryosolution.
>
> And a few wild ideas to continue the discussion that is very important as the ligands are
> always very difficult to identify.
>
> Example: If you have 1.5 M ammonium sulfate you should consider hydrated ammonium ions
> H3O+ + NH3 in equilib. H2O + NH4+
> The pH will determine the equilibrium point and NH4+ would be a good ligand for a carboxylate.
> Assuming 200mM Li2SO4:
>
> A lithium ion (H20-Li-H20 with a Li-O distance of 2.14 Ang) Li+ is often associated with more that two H2O molecules
> with an angle of 105° not 180° but cannot be excluded in proximity of a carboxylate where the environ ment could be
> distorted (not very believable).
>
> (H2O, Na+ and Mg++ 10 electrons) water is always the most probable.
> 2 H2O in equilib. OH- + H3O+
> Carboxylates are often destroyed by radiation damage.
>
> The most probable ligand will be at high concentration in the mother liquor the moment
> the crystal was flashcooled.
> This is rarely the case for typically 0.02% azide (I would made an exception in proximity to Cu++, Fe++ or Zn++ ions).
> Azide -N=N+=N- is also suspitious as a negative ion is a bad counterion for a carboxylate.
>
> Enrico.
>
>
> On Mon, 08 Jul 2013 11:19:46 +0200, <[log in to unmask]> wrote:
>
>> Dear Ed,
>>
>> What is the pH of your crystallization buffer? If it is acidic, either the azide or the carboxylate may be protonated.
>> Also the local environment of the carboxylate can make a hugh difference in PKa. You could also use some Bayesian
>> logic: given the elongated linear density, what else of the available components of your crystallization drop would fit?
>>
>> Best,
>> Herman
>>
>> -----Ursprüngliche Nachricht-----
>> Von: CCP4 bulletin board [mailto:[log in to unmask]] Im Auftrag von Edward A. Berry
>> Gesendet: Sonntag, 7. Juli 2013 22:21
>> An: [log in to unmask]
>> Betreff: [ccp4bb] help identifying ligand
>>
>> In a structure I'm refining, there are a couple of oblong blobs associated with carboxylates.
>> (screenshots at http://sb20.lbl.gov/berry/ccp4/azide/)
>> If I modeled with two waters, they refine too close together for normal H-bond,
>> 2.3 to 2.5 A; and their density is connected.
>>
>> I considered one water with alternate locations, but the distal position wouldn't make much sense if the proximal
>> water wasn't there. The density is the right size for azide, which was present in the medium, but I expect a chemist
>> would find it unreasonable to have anionic azide (pKa of hydrazoic acid ~4.6) associating with a carboxylate.
>> Would that make sense? or does anyone have other suggestions?
>> (resolution is 2.2A, contour 0.25 e/A^3 or about 1.3 sigma)
>>
>> Thanks,
>> Ed
>
>
|