Inclusion of hydrogens---when and how

Hydrogen atoms are an important part of protein stmctures as they determine many of the non-bonded interactions, and in many cases they are the key players in catalytic events. Due to their small scattering power, hydrogen atoms are difficult to detect in electron density maps at less than atomic resolution. However, at atomic resolution many hydrogen atoms can be positively identified in difference electron density maps and then modeled with confidence. 

From a teclmical point of view, the inclusion of hydrogens nearly doubles the number of atoms for which stmcture factor calculations have to be performed and thus leads to a sigiuficant cost in terms of computing time. Given that the inclusion of hydrogen usually only leads to a relatively small improvement in refinement statistics (typical drops in Fwork and Ffree are on the order of 0.5-1.0%) and clarity of the electron density maps, it is therefore advisable to only include hydrogen atoms at the later stages of refinement for the sake of efficiency. 

Note that this set of statements will also generate the requested hydrogens for histidine residues with atoms in multiple conformations. 

Concerning the actual positions of hydrogen atoms placed by SHELXL, some caution may be necessary when distances between these hydrogens and other atoms are measured as SHELXL places the hydrogen atoms into a position that is optimal for refinement against X-ray diffraction data. These positions do not correspond to the actual centre of the nucleus of the hydrogen atom (see also Chapter 3 of this book). 

As in standard refinements of macromolecules, the modeling of ordered solvent molecules is an iterative process in which it is important to adhere to some mles in order to arrive at a consistent description and to avoid endless cycling  

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