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, <herman.schreu...@sanofi.com> 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:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
Edward A. Berry
Gesendet: Sonntag, 7. Juli 2013 22:21
An: CCP4BB@JISCMAIL.AC.UK
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
--
Enrico A. Stura D.Phil. (Oxon) , Tel: 33 (0)1 69 08 4302 Office
Room 19, Bat.152, Tel: 33 (0)1 69 08 9449 Lab
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e-mail: est...@cea.fr Fax: 33 (0)1 69 08 90 71
