Diffractograph: single-particle reconstruction using electron-diffraction data

Abstract

We recently showed that narrow-beam electron diffraction of single particles provides higher signal-to-noise ratios and lower radiation damage than imaging. Here we introduce Diffractograph, a suite for reconstructing three-dimensional structure from these data. Diffractograph selects mutually compatible diffraction frames, groups them into one or more models and discards incompatible frames. In the ab initio workflow, this is done without prior structural information. In the reference-guided workflow, a low-resolution electrostatic potential map from single-particle cryo-EM is used to select compatible frames and determine their orientations. The oriented frames are combined into a three-dimensional intensity distribution. The reference map supplies low-resolution phases for the oversampled structure factors, and density modification extends these phases to higher resolution. For synthetic 200-keV diffraction data extending to 2.2 A, Diffractograph retained all frames and recovered the correct orientation of every retained frame with a median plane-normal error of 0.27 degrees. These results establish a computational workflow for structure determination using single-particle electron-diffraction data.