Even though SHELXL refinements often involve resolutions of 1.5A or better, I discourage SHELXL users from depositing their hydrogen coordinates. There are three reasons:
1. The C-H, N-H and O-H distances required to give the best fit to the electron density are significantly shorter than those required for molecular modeling and tests on non-bonded interactions (or located by neutron diffraction). It is ESSENTIAL to recalculate them hydrogens at longer distances before using MolProbity and other validation software. 2. There is considerable confusion concerning the names to be assigned to the hydrogens. This is not made easier by the application of a chirality test to -CH2- groups! 3. O-H hydrogens are particularly difficult to 'see' and the geometrical calculation of their positions is often ambiguous. The same applies to the protonation states of histidines and carboxylic acids. In addition such hydrogen positions are often disordered. For refinement I recommend including C-H and N-H but not O-H hydrogens. For very high resolution structures this reduces Rfree by 0.5-1.0% and clearly improves the model. At all resolutions the antibumping restraints involving hydrogens are useful. 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, 14 Sep 2010, Dr. Mark Mayer wrote: > Here's one for the community, which I'll post to both Phenix and CCP4 BBs. > > Where does the crystallographic community stand on deposition of coordinates > with riding hydrogens? > Explicit H are required for calculating all atom clash scores with Molprobity, > and their use frequently gives better geometry (especially at low resolution). > Phenix uses explicit riding H for refinement, and outputs these in the refined > PDB. Refmac also uses riding H but does not output H coordinates. > > While depositing a series of structures refined at 1.4 - 2.75 A with Phenix > got the following email from the RCSB, who asked I resupply coordinates > without H for two of the structures. Since we can't see H even at 1.4 Å I > don't understand why an arbitrary cut off of 1.5 Å was chosen, and also why > explicit H atoms used in refinement and geometry validation should be stripped > from the file. > > FROM RCSB > > We encourage depositors not to use hydrogens in the final PDB file for > the low resolution structures (> 1.5 A). Please provide an updated PDB > file. We request you to use processed PDB file as a starting point for > making any corrections to the coordinates and/or re-refinement. > -- > > Mark > >
