Why electron density?
What we see as the result of a crystallographic experiment is not really a picture of the atoms, but a map of the distribution of electrons in the molecule, i.e. an electron density map. However, since the electrons are mostly tightly localised around the nuclei, the electron density map gives us a pretty good picture of the molecule. This is because electromagnetic radiation (including X-rays) interacts with matter through its fluctuating electric field, which accelerates charged particles. You can think of the electrons fluctuating in position and, through their accelerations, emitting electromagnetic radiation in turn. Because electrons have a much higher charge to mass ratio than atomic nuclei or even protons, they are much more efficient in this process. Intensity of scattered radiation is proportional to the square of the charge/mass ratio, and the proton is about 2000 times as massive as the electron.
