I have rarely worked with such data, but when we did, we always kept to
the riding hydroge positions in for refinement. You can check the
important ones by calculating sfs without them and seeing how well they
fit the map. For important residues like ASPS in catalytic triads that
can be very revealing.
Eleanor
On 11/23/2010 02:12 PM, Mischa Machius wrote:
We have a similar case. There is difference density, but only for some of the
hydrogens (mostly methyl groups on Leu, Ile, Val, Ala). How does one decide
which hydrogens to include in explicit refinement? The case in question has
0.99Å data (diffraction is significantly better, but data were collected to
only 0.99Å).
n model, but for the important ock whether the riding posnes, we would che
Sorry, first time refining at that kind of resolution.
Thanks! MM
On Nov 23, 2010, at 3:03 AM, George M. Sheldrick wrote:
Even with SHELX, at 1.2A you should use a riding model for hydrogens and
not refine them freely. SHELX has a useful facility (OMIT $H or OMIT
followed by specific hydrogen atom names) to keep the hydrogen atoms in
the atom list but not include their contributions to the structure
factors. Then you can very easily see in a difference map (e.g. with
COOT) if there is density near their expected positions.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-22582
On Tue, 23 Nov 2010, Ed Pozharski wrote:
Not sure if all the sirs will concur (and it might be a good idea to ask
madams also), but the answer is probably no. As far as protonation
state goes (guess that is what you are after, not oxidation), a better
strategy may be to look into the bond lengths between the appropriate
heavy atoms that are affected by it. Make sure that you refine without
restraints imposed on a particular bond and see if its length is closer
to the one corresponding to protonated or deprotonated state.
Cheers,
Ed.
On Mon, 2010-11-22 at 23:18 -0600, Kenneth Satyshur wrote:
Sirs:
We are attempting to refine hydrogens on a ligand (which is 100 % occupied) and
has ~ 40 heavy atoms (CNO). The data is 1.2 A, 325 AA, 83335 data points in C2.
We have refined aniso and with H riding along (Rf= 17, R = 15) in CCP4. Can we
individually
refine the protons on the ligand? Let them run free with the others along for
the ride?
Or will they just run away at this
resolution? Can CCP4 even do this? Should we switch to Shelx or Phenix?
It is important to find out what the oxidation state is for the ligand at the pH
we crystallized the protein and complex.
thanks
-----------------------------------------------------------------------
Mischa Machius, PhD
Director, Center for Structural Biology
Assoc. Professor, Dept. of Pharmacology
Member, Lineberger Comprehensive Cancer Center
University of North Carolina
4079 Genetic Medicine
CB#7365
120 Mason Farm Road
Chapel Hill, NC 27599-7365, U.S.A.
tel: +1-919-843-4485
fax: +1-919-966-5640
email: mach...@unc.edu
