Continuous Serial Electron Diffraction for High Quality Protein Structures

Abstract

Determining macromolecular structures is crucial for understanding biological mechanisms and advancing drug discovery. Three-dimensional electron diffraction (3D ED), also known as microcrystal electron diffraction (MicroED) using continuous sample rotation has emerged as a powful method for solving structures from sub-micrometre-sized crystals. However, the resolution of MicroED data from protein crystals is often limited by radiation damage. Serial electron diffraction (SerialED) overcomes this limitation by merging single-shot diffraction patterns from thousands of crystals, but its widespread use has been hindered by the complexity and scarcity of equipment required for single shot data acquisition. Here, we introduce continuous SerialED (c-SerialED) - a simple, robust and widely accessible protocol. This approach collects diffraction data quickly and efficiently from all crystals within a given area, without prior crystal identification. We show that only using a standard cryo-EM instrument equipped with a simple widely available CMOS detector, c-SerialED greatly reduces radiation damage while improving the data quality. We demonstrate that c-SerialED enables determination of lysozyme structures at atomic resolution (0.83 [A]) and improves the data resolution of Dype Type Peroxidase Aa (DTPAa) crystals from 2.5 [A] (MicroED) to 1.3 [A]. Remarkably, the resulting structures are virtually free of radiation damage. The improved data quality and resolution allow visualization of radiation sensitive chemical features and protein-ligand interactions to state-of-the-art accuracy. By providing a convenient, fast, and damage-minimizing workflow on existing cryo-EM setups, c-SerialED significantly enhances the applicability of electron diffraction in structural biology. We anticipate our protocol will enable a wide range of studies requiring high-quality diffraction data from radiation-sensitive macromolecular crystals.