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. 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.
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.