Protein structure determination by electron diffraction using a single three‐dimensional nanocrystal

Three‐dimensional nanometre‐sized crystals of macromolecules currently resist structure elucidation by single‐crystal X‐ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg‐white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular‐replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side‐chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in‐house‐designed 1024 × 1024 pixel Timepix hybrid pixel detector for low‐dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high‐energy electrons from X‐rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. A single three‐dimensional protein nanocrystal was used for structure determination by electron diffraction. Data were acquired using the rotation method with a Timepix hybrid pixel detector for low‐dose data acquisition.