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, <[email protected]> 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:[email protected]] Im Auftrag von Edward
A. Berry
Gesendet: Sonntag, 7. Juli 2013 22:21
An: [email protected]
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
