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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.

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  • $\begingroup$ Welcome to Chemistry.SE! Take the tour to get familiar with this site. Mathematical expressions and equations can be formatted using $\LaTeX$ syntax. With X-ray crystallography you measure electron density, for light elements the uncertainty is probably too high to depict their position accurately. Have a look at this file, maybe it helps you a little until you receive an answer. $\endgroup$ – Martin - マーチン♦ Mar 22 '16 at 5:17
  • $\begingroup$ Related: How to add hydrogens to a crystal structure? $\endgroup$ – andselisk♦ Oct 9 '17 at 12:16
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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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  • $\begingroup$ Ok, this makes sense. I never would have guessed it had to do with the measurement/ imaging of the molecule. Thanks for the answer. $\endgroup$ – Crash McLarson Mar 22 '16 at 5:38

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