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Hi Pietro,
A while ago, I had a chance to work with an ultra-high resolution
(0.86 Ang) of a small protein, BPTI (Acta Crystallogr., 2001, D57,
649-663). We have done few experiments on that data. One such was
dealing with H-atoms. We could locate several H-atoms in the
difference density map in the core of the protein, particularly on
the C-alpha and the amide N atoms (on some water molecules too!). We
added them as riding atoms in the SHELXL. To our surprise, there was
still some density near the H-atoms. We realized that the position of
some of the H-atoms, particularly on C-alpha's in a beta strand is in
fact is not at the predicted position but is offset by 0.1 to 0.2 Ang
in the direction towards a carbonyl oxygen in the neighboring strand.
We concluded that this offset is because of the possible C-H...O
hydrogen which is less accepted in biocrystallographer community.
I like your idea of adding H-atoms (probably not refining them but
only as riding, may be at resolutions better than 1.0 Ang.). But keep
in mind that not all the H-atoms are NOT in the ideal positions.
Happy hydrogenation!
Anthony
________________________________
Anthony Addlagatta, PhD
HHMI Research Associate
Institute of Molecular Biology
University of Oregon
Eugene, OR-97403
Phone: (541) 346-5867
Fax: (541)346-5270
Web: http://darkwing.uoregon.edu/~anthony
On Jan 13, 2007, at 6:56 AM, Pietro Roversi wrote:
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Dear all,
let's see if I can make a smooth transition of the
bulletin board to a different topic.
Marc Schiltz mentioned that H atoms are not routinely
refined because more often than not the resolution of the data does
not warrant their refinement - except I think there are a few H
atoms in proteins whose positions _are_ uniquely defined by the
position of the atom thy are bonded to, and the atoms bonded to
that e.g. the amide Hs, and the Hs on the Calpha, Asn and Gln amide
Hs, Proline Hs, and so on. In fact, most Hs are a pretty sure bet
except the Ser, Tyr and Thr -OH moieties, the -SH of Cys, the
terminal -CH3 of Ala, Met, Ile, Val, Leu, Thr, and the ones bound
to N on Arg, Lys, His side chains. Some stereochemical guesswork
could be done on those but I do not want to open a can of worms there.
Anyway, those H atoms could be added at positions that are
essentially correct within the typical resolution of the data, at
zero parameter cost. They scatter, there are quite a few of them,
and they would actually provide extra non-bonded restraints given
that the H-X bond has a direction and a length (for example
MolProbity uses H atom addition to detect clashes pointing to
suboptimal parts of the model). This is a case of a very reliable
prior which we should incorporate all the more in our model, given
that the data are uninformative as to that part of the model.
This is already done for example in Shelx with riding H atoms
- so an option that would "add safely locatable Hydrogens" would
help all refinement programs.
As the Morris cars fans magazine's title goes: "Minor Matters"
Ciao
Pietro
