I would like to suggest to read this paper entitled: Electron Diffraction Using Transmission Electron Microscopy [J. Res. Natl. Inst. Stand. Technol. 106, 997–1012 (2001)]
there are some differences and similarities compared to X-ray crystallography.
1. Your samples will need to be about 100-200nm thin and have to be vitrified to withstand the vacuum of an electron microscope. Vitrification is broadly used in Cryo-EM.
2. You will need a sensitive detector capable of collecting diffraction patterns at extremely low dose. We used a Timepix Detector, now marketed by Amsterdam Scientific Instruments.
3. You can collect rotation data like you would with X-Ray Crystallography and use X-ray programs to solve the structure.
Please also look at our Acta paper for more info on sample prep and data collection and analysis.
Good luck! feel free to e-mail me if you have any further questions.