Abstract
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
Highlights
Transmission electron microscopy as a tool for both material and life science has recently seen revolutionary developments, driven by new types of electron detectors, computational data analysis, automation, and sample preparation
Statistics from the Protein Data Bank (PDB) and the Electron Microscopy Data Bank (EMDB) show a clear increase in the number of protein structures that are recovered through electron-based techniques
While a large portion of steps to process serial crystallography data have been addressed in established packages such as CrystFEL (White et al, 2012), cctbx.xfel (Hattne et al, 2014), and nXDS (Kabsch, 2014), SerialED processing requires some more specific steps, which we will discuss in more detail
Summary
Transmission electron microscopy as a tool for both material and life science has recently seen revolutionary developments, driven by new types of electron detectors, computational data analysis, automation, and sample preparation. Single-particle analysis is limited in its scope to molecules of weight above ≈ 40 kDa as the signal-to-noize ratio of such small particles in electron micrographs is not sufficient for computational alignment (Henderson, 1995; Glaeser, 2019), and despite recent progress in CryoEM (Nakane et al, 2020; Yip et al, 2020), X-ray crystallography is still clearly predominant for routine structure determination at the atomic resolution scale Diffractive electron techniques such as crystallography of monolayers of proteins (2D crystallography) led to seminal results (Henderson and Unwin, 1975; Henderson et al, 1990; Gonen et al, 2005), but remained limited in scope as preparation of suitable two-dimensional crystals is often prohibitively difficult. Discussion and Outlook reviews various specific aspects and potential issues of our approach, and future directions of further development
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