scholarly journals Optimization of rotation electron diffraction data collection and data processing

2015 ◽  
Vol 71 (a1) ◽  
pp. s404-s404
Author(s):  
Magdalena O. Cichocka ◽  
Jie Su ◽  
Wei Wan ◽  
Xiaodong Zou
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Data Processing ◽  
Diffraction Data ◽  
Electron Diffraction Data

scholarly journals Single Crystal 3D Rotation Electron Diffraction from Nano-sized Crystals

2014 ◽  
Vol 70 (a1) ◽  
pp. C366-C366
Author(s):  
Xiaodong Zou
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Data Processing ◽  
Single Crystal ◽  
Diffraction Data ◽  
Structure Determination ◽  
Reciprocal Lattice ◽  
Electron Diffraction Data ◽  
Electron Crystallography ◽  
Structure Solution

Electron crystallography is an important technique for structure analysis of nano-sized materials. Crystals too small or too complicated to be studied by X-ray diffraction can be investigated by electron crystallography. However, conventional TEM methods requires high TEM skills and strong crystallographic knowledge, which many synthetic materials scientists and chemists do not have. We recently developed the software-based Rotation Electron Diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Complete single crystal 3D electron diffraction data can be collected from nano- and micron-sized crystals in less than one hour by combining electron beam tilt and goniometer tilt, which are controlled by the RED – data collection software.3 The unit cell, possible space groups and electron diffraction intensities can be obtained from the RED data using the RED data processing software. The figure below illustrates the data collection and data processing of a zeolite silicalite-1 by RED. 1427 ED frames were collected in less than 1 hour from a crystal of 800 x 400 x 200 nm in size. A 3D reciprocal lattice of silicalite-1 was reconstructed from the ED frames, from which the unit cell parameters and space group were determined (P21/n, a=20.02Å, b=20.25Å, c=13.35Å, alfa=90.130, beta=90.740, gamma=90.030. It was possible to cut the 3D reciprocal lattice perpendicular to any directions and study the reflection conditions. The reflection intensities could be extracted. The structure of the calcined silicalite-1 could be solved from the RED data by routine direct methods using SHELX-97. All 78 unique Si and O atoms could be located and refined to an accuracy better than 0.08 Å. The RED method has been applied for structure solution of a wide range of crystals and shown to be very powerful and efficient. Now a structure determination can be achieved within a few hours, from the data collection to structure solution. We will present several examples including unknown inorganic compounds, metal-organic frameworks and organic structures solved from the RED data. Different parameters that affect the RED data quality and thus the structure determination will be discussed. The methods are general and can be applied to any crystalline materials.

scholarly journals A Medipix quantum area detector allows rotation electron diffraction data collection from submicrometre three-dimensional protein crystals

2013 ◽  
Vol 69 (7) ◽  
pp. 1223-1230 ◽  
Author(s):  
Igor Nederlof ◽  
Eric van Genderen ◽  
Yao-Wang Li ◽  
Jan Pieter Abrahams
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Diffraction Data ◽  
Three Dimensional ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Electron Diffraction Data ◽  
Single Shot ◽  
X Ray ◽  
Area Detector

When protein crystals are submicrometre-sized, X-ray radiation damage precludes conventional diffraction data collection. For crystals that are of the order of 100 nm in size, at best only single-shot diffraction patterns can be collected and rotation data collection has not been possible, irrespective of the diffraction technique used. Here, it is shown that at a very low electron dose (at most 0.1 e− Å−2), a Medipix2 quantum area detector is sufficiently sensitive to allow the collection of a 30-frame rotation series of 200 keV electron-diffraction data from a single ∼100 nm thick protein crystal. A highly parallel 200 keV electron beam (λ = 0.025 Å) allowed observation of the curvature of the Ewald sphere at low resolution, indicating a combined mosaic spread/beam divergence of at most 0.4°. This result shows that volumes of crystal with low mosaicity can be pinpointed in electron diffraction. It is also shown that strategies and data-analysis software (MOSFLMandSCALA) from X-ray protein crystallography can be used in principle for analysing electron-diffraction data from three-dimensional nanocrystals of proteins.

Specifics of the data processing of precession electron diffraction tomography data and their implementation in the program PETS2.0

2019 ◽  
Vol 75 (4) ◽  
pp. 512-522 ◽  
Author(s):  
Lukáš Palatinus ◽  
Petr Brázda ◽  
Martin Jelínek ◽  
Jaromíra Hrdá ◽  
Gwladys Steciuk ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Processing ◽  
Diffraction Data ◽  
Crystal Orientation ◽  
Diffraction Method ◽  
Specific Aspect ◽  
Electron Diffraction Data ◽  
Diffraction Tomography ◽  
Profile Fitting ◽  
Precession Electron Diffraction

Electron diffraction tomography (EDT) data are in many ways similar to X-ray diffraction data. However, they also present certain specifics. One of the most noteworthy is the specific rocking curve observed for EDT data collected using the precession electron diffraction method. This double-peaked curve (dubbed `the camel') may be described with an approximation based on a circular integral of a pseudo-Voigt function and used for intensity extraction by profile fitting. Another specific aspect of electron diffraction data is the high likelihood of errors in the estimation of the crystal orientation, which may arise from the inaccuracies of the goniometer reading, crystal deformations or crystal movement during the data collection. A method for the refinement of crystal orientation for each frame individually is proposed based on the least-squares optimization of simulated diffraction patterns. This method provides typical angular accuracy of the frame orientations of less than 0.05°. These features were implemented in the computer program PETS 2.0. The implementation of the complete data processing workflow in the program PETS and the incorporation of the features specific for electron diffraction data is also described.

scholarly journals High-throughput continuous rotation electron diffraction data acquisition via software automation

2018 ◽  
Vol 51 (6) ◽  
pp. 1652-1661 ◽  
Author(s):  
Magdalena Ola Cichocka ◽  
Jonas Ångström ◽  
Bin Wang ◽  
Xiaodong Zou ◽  
Stef Smeets
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
High Throughput ◽  
Diffraction Data ◽  
Human Error ◽  
Electron Diffraction Data ◽  
Transmission Electron ◽  
Electron Diffraction Technique ◽  
Continuous Rotation ◽  
Crystal Electron

Single-crystal electron diffraction (SCED) is emerging as an effective technique to determine and refine the structures of unknown nano-sized crystals. In this work, the implementation of the continuous rotation electron diffraction (cRED) method for high-throughput data collection is described. This is achieved through dedicated software that controls the transmission electron microscope and the camera. Crystal tracking can be performed by defocusing every nth diffraction pattern while the crystal rotates, which addresses the problem of the crystal moving out of view of the selected area aperture during rotation. This has greatly increased the number of successful experiments with larger rotation ranges and turned cRED data collection into a high-throughput method. The experimental parameters are logged, and input files for data processing software are written automatically. This reduces the risk of human error, and makes data collection more reproducible and accessible for novice and irregular users. In addition, it is demonstrated how data from the recently developed serial electron diffraction technique can be used to supplement the cRED data collection by automatic screening for suitable crystals using a deep convolutional neural network that can identify promising crystals through the corresponding diffraction data. The screening routine and cRED data collection are demonstrated using a sample of the zeolite mordenite, and the quality of the cRED data is assessed on the basis of the refined crystal structure.

scholarly journals Electron diffraction data processing with DIALS

2018 ◽  
Vol 74 (6) ◽  
pp. 506-518 ◽  
Author(s):  
Max T. B. Clabbers ◽  
Tim Gruene ◽  
James M. Parkhurst ◽  
Jan Pieter Abrahams ◽  
David G. Waterman
Keyword(s):  
Electron Diffraction ◽  
Data Integration ◽  
Data Processing ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Beam Model ◽  
Detector Distance ◽  
Diffraction Geometry ◽  
Continuous Rotation ◽  
Ewald Sphere

Electron diffraction is a relatively novel alternative to X-ray crystallography for the structure determination of macromolecules from three-dimensional nanometre-sized crystals. The continuous-rotation method of data collection has been adapted for the electron microscope. However, there are important differences in geometry that must be considered for successful data integration. The wavelength of electrons in a TEM is typically around 40 times shorter than that of X-rays, implying a nearly flat Ewald sphere, and consequently low diffraction angles and a high effective sample-to-detector distance. Nevertheless, the DIALS software package can, with specific adaptations, successfully process continuous-rotation electron diffraction data. Pathologies encountered specifically in electron diffraction make data integration more challenging. Errors can arise from instrumentation, such as beam drift or distorted diffraction patterns from lens imperfections. The diffraction geometry brings additional challenges such as strong correlation between lattice parameters and detector distance. These issues are compounded if calibration is incomplete, leading to uncertainty in experimental geometry, such as the effective detector distance and the rotation rate or direction. Dynamic scattering, absorption, radiation damage and incomplete wedges of data are additional factors that complicate data processing. Here, recent features of DIALS as adapted to electron diffraction processing are shown, including diagnostics for problematic diffraction geometry refinement, refinement of a smoothly varying beam model and corrections for distorted diffraction images. These novel features, combined with the existing tools in DIALS, make data integration and refinement feasible for electron crystallography, even in difficult cases.

scholarly journals Putting MicroED to the Test: An Account of the Evaluation of 30 Diverse Pharmaceutical Compounds

2021 ◽  
Author(s):  
Jessica E. Burch ◽  
Austin G. Smith ◽  
Seb Caille ◽  
Shawn D. Walker ◽  
Ryan Wurz ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Electron Diffraction ◽  
Sample Preparation ◽  
Data Processing ◽  
Diffraction Data ◽  
Structural Data ◽  
Pharmaceutical Compounds ◽  
Electron Diffraction Data ◽  
Transfer Processes ◽  
Minimal Sample

The application of microcrystal electron diffraction (microED) to a variety of pharmaceutical compounds is reported. The examples and work detailed showcase the utility of microED as a routine technique for the rapid collection, analysis, and generation of structural data on a number of pharmaceutically relevant compounds, requiring minimal sample preparation and often without the need for time-consuming vitrification and cryo transfer processes. The development of a scripted data processing workflow allowed for simultaneous collection and processing of electron diffraction data, further expediting structural analysis of fifteen compounds.

scholarly journals Complete 3D electron diffraction data collection - new methods and applications

2010 ◽  
Vol 66 (a1) ◽  
pp. s67-s67
Author(s):  
Xiaodong Zou ◽  
Peter Oleynikov ◽  
Daliang Zhang ◽  
Tom Willhammar ◽  
Sven Hovmöller
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
New Methods ◽  
3D Electron

scholarly journals InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction

2020 ◽  
Vol 53 (5) ◽  
pp. 1217-1224
Author(s):  
Maria Roslova ◽  
Stef Smeets ◽  
Bin Wang ◽  
Thomas Thersleff ◽  
Hongyi Xu ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Data Collection ◽  
Data Acquisition ◽  
Diffraction Data ◽  
Electron Diffraction Data ◽  
Electron Dose ◽  
Structure Solution ◽  
Continuous Rotation ◽  
Thermo Fisher Scientific ◽  
Cross Platform

A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.

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