Both techniques give you the average electron density over thousands to billions of molecules. The difference is in what kind of data you actually collect, and

Both techniques give you the average electron density over thousands to billions of molecules. The difference is in what kind of data you actually collect, and how you process and combine the data to get that averaged map: - In X-ray crystallography, you're collecting the amplitudes of the Fourier transform of the electron density in the repeating unit of the crystal. The fact that it's a well-ordered (usually) crystal effectively "amplifies" the FT, and you get a series of images like this (from one orientation of the crystal): https://cdn.britannica.com/02/147302-050-3F732246/X-ray-diffraction-pattern-enzyme.jpg https://cdn.britannica.com/02/147302-050-3F732246/X-ray-diff... - In EM, you're collecting direct images of particles randomly distributed on a grid, but they're 2D and individually very noisy, like this: https://www.pnas.org/content/pnas/110/45/18037/F3.large.jpg?width=800&height=600&carousel=1 https://www.pnas.org/content/pnas/110/45/18037/F3.large.jpg?... In either case, there's a lot of complex math that goes into reconstructing the electron density - but the end result, the electron density map, is very similar (aside from the absence of crystal packing interactions in the EM map).