Research Article: Electron diffraction data processing with DIALS

Date Published: June 01, 2018

Publisher: International Union of Crystallography

Author(s): Max T. B. Clabbers, Tim Gruene, James M. Parkhurst, Jan Pieter Abrahams, David G. Waterman.


Adaptations to the DIALS package are described that make it a suitable choice for processing challenging continuous-rotation electron diffraction data. The results of using the extended package are presented for a case consisting of seven example data sets.

Partial Text

Electron diffraction (ED) allows the structural analysis of nanometre-sized samples of crystalline material. Since the maximal radiation dose is proportional to the sample volume, electron diffraction of organic and macromolecular compounds was long limited to two-dimensional samples (Unwin & Henderson, 1975 ▸; Hovmöller, 2017 ▸). In contrast to X-ray crystallography, the three domains, inorganic, organic and macromolecular electron crystallography, developed rather independently of each other (Vainshtein, 1964 ▸; Dorset, 1995 ▸; Kolb et al., 2007 ▸; Glaeser et al., 2007 ▸; Zou et al., 2011 ▸). Physical and instrumental limitations, such as miniature sample size or dynamic scattering effects and lens distortions, affect data precision. However, several studies show that the model accuracy compares with that of X-ray structures (Weirich et al., 1996 ▸; Mugnaioli & Kolb, 2014 ▸; Dorset, 1995 ▸; Palatinus et al., 2017 ▸). Only about one and a half decades ago, electron diffraction of three-dimensional crystals was pioneered with automated diffraction tomography (ADT) and was further refined with rotation electron diffraction (RED; Kolb et al., 2007 ▸; Zhang et al., 2010 ▸; Gemmi et al., 2015 ▸). Recently, single-crystal three-dimensional electron diffraction has also been applied to protein crystals by using the standard rotation method (Nederlof et al., 2013 ▸; Hattne et al., 2015 ▸; Yonekura et al., 2015 ▸; Clabbers et al., 2017 ▸). The only very recent use of integration software with profile fitting and scaling is indicative of the independent development of electron diffraction. These methods have been in use for decades in X-ray crystallography, improving the quality of diffraction intensities and their standard uncertainties, whilst enabling heuristic correction for systematic errors (Pflugrath, 1999 ▸; Leslie, 1999 ▸).

Electron diffraction from three-dimensional crystals has recently been used to solve the structures of macromolecules such as proteins. Previous authors have shown that where data are collected using the rotation method, as is standard in X-ray crystallography, data-processing software such as MOSFLM and XDS can be employed to successfully integrate the Bragg peaks. Here, we show that the DIALS package, with appropriate adaptations, is also a viable alternative, even for difficult data sets with problematic features such as distortions caused by microscope lens systems and drift of the direct beam position. A set of seven example data sets was successfully processed using DIALS, and the specific decisions required at each step are described in detail. The quality of data integrated with DIALS is very similar to what could be achieved with XDS (Clabbers et al., 2017 ▸).




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