Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination.

Bin Wang,Stef Smeets,Xiaodong Zou

doi:10.1107/s2052252519007681

Bin Wang, Stef Smeets + Show 1 more

Open Access

https://doi.org/10.1107/s2052252519007681

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Journal: IUCrJ	Publication Date: Jul 12, 2019
Citations: 67	License type: CC BY 4.0

Affiliation: Stockholm University

Abstract

Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal-organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool.

Highlights

Understanding the arrangement of atoms in solids, whether of materials science or life science interest, is often key to understanding their nature and function
Clustering methods were initially developed for high-throughput X-ray beamlines at synchrotrons to study biological samples (Giordano et al, 2012; Foadi et al, 2013). We find that these methods can be applied well in the context of multi-crystal electron diffraction, such as the automated data collections that are the focus of this study, and when dealing with a large number of manually collected datasets
We describe the development of SerialRED, an extension of the serial electron crystallography method (Smeets et al, 2018b) by integrating a continuous rotation in combination with an automated tracking routine

Summary

Introduction

Understanding the arrangement of atoms in solids, whether of materials science or life science interest, is often key to understanding their nature and function. The capability of electron diffraction (ED) for structure determination has been demonstrated on a large variety of samples, for example inorganic (Kolb et al, 2010; Jiang et al, 2011; Martınez-Franco et al, 2013; Smeets et al, 2013, 2014; Su et al, 2014), organic (Kolb et al, 2010; Gorelik et al, 2012; Zhang et al, 2013; Gruene et al, 2018b; Jones et al, 2018) and protein crystals (Shi et al, 2013; Yonekura et al, 2015; Clabbers et al, 2017; Xu et al, 2018; Lanza et al, 2019) For this reason, the method has recently attracted a great deal of attention (Brown & Clardy, 2018). All of the above methods have shown great ability in terms of structure determination of nano-sized crystals (Yun et al, 2015)

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