Why are there no hydrogen atoms in the crystal structure of a biomolecule?
Typically crystal structures are determined by X-ray diffraction off of electrons within a bond and around the nuclei of each atom. Since H only has 1 electron, and its often involved in a polar type bond (hence doesn't spend much time by the H nucleus when bonded) it is notoriously hard to "see" with X-rays. 

In order to have X-rays diffract accurately off H atoms the sample crystal needs to be large and very regular; this is not usually the case with proteins. As a workaround information about the H position can be calculated by the other atoms hybridization. This is often unreliable especially with all the hydrogen bonding in proteins which pulls them out of their idealized positions.