In crystallography, including other approaches to resolve protein structures, is there any explanation why the wavelength that we use must equal to interatomic distances?
The answer for your question is simple: one cannot see anything that is smaller than incident wavelength. To be precise, the wavelength must be equal or smaller than smallest interatomic distance.
Same thing applies to optical microscopy. It is not possible (excluding some tricks) to see something that is smaller than visible light wavelength.
Well it is not exactly that when the object you want to observe (or two objects separated by a small distance) will not scatter incident light at all when lightwave is longer than object itself. Some part of light will scatter anyway but the amount of details that you can observe will suffer strongly.
For further explaination of this interesting problem try to look for so-called abbe limit.
Quick (but not very deep) explaination https://en.wikipedia.org/wiki/Diffraction-limited_system