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I think that there is another possible explanation for your displaced
hydrogen atom that is involved in a C-H...O hydrogen bond. When SHELXL
was written many years ago such hydrogen bonds were not generally
accepted, so when the BUMP instruction is used to apply antibumping
restraints no special action is taken (as it would have been for O-H..O
etc.) to avoid the H and O from pushing each other apart. So your
hydrogen atom has probably been pushed out of its density, with
undesirable effects on the rest of the structure, because the riding
model does not allow the angles at the C atom to vary to take up the strain.
The only easy remedy is to remove the BUMP instruction, you don't need
it with 0.86A data anyway. This may well reduce the free R too.
There are similar but more severe problems when SHELXL stupidly tries to
place two H atoms on the same O-H...O hydrogen bond (H...H antibumping
causes serious distortions of the rest of the structure), which is why I
recommend not including O-H hydrogens (and N-H in histidine rings).
George
Anthony Addlagatta wrote:
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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
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
