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).
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
