Why are there no hydrogen atoms in the crystal structure of a biomolecule?

I am taking a physics and chemistry at the nanoscale class at my university and for a project I must learn how to use Visual Molecular Dynamics (VMD). One of the models involved in this project is apo-core-streptavidin in complex with biotin at pH 4.5 (1SWE.pdb). The crystal structure can be found [protein data bank](http://www.rcsb.org/pdb/explore/explore.do?structureId=1SWE). There are no hydrogen atoms in this file/model and I was wondering why that is. I can't find the answer to this anywhere online.




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. 


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Hydrogens don't diffract X-rays to the same extent (basically not at all) as compared to other atoms, so they do not show up in normal X-ray crystallography because their signal is so small.


This is because the electrons are actually responsible for diffraction and most other bio-elements have many more electrons than hydrogen, so their scattering signals are much larger than those for hydrogen.


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