3D Electron Diffraction: The Nanocrystallography Revolution

Gemmi, Mauro; Mugnaioli, Enrico; Gorelik, Tatiana E.; Kolb, Ute; Palatinus, Lukáš; Boullay, Philippe; Hovmöller, Sven; Abrahams, Jan Pieter

doi:10.1021/acscentsci.9b00394

Cited by 401 publications

(360 citation statements)

References 176 publications

(595 reference statements)

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“…However, in the relativistic UED demonstrations, the minimum electron beam size on the sample was 300 µm with a 300-µm-diameter condenser aperture, which is still unsuitable for microcrystal electron diffraction (micro ED) or now emerging three-dimensional electron diffraction (3D ED) [32]. In the next challenge, we propose a small condenser aperture (50 µm or less) to collimate the electron beam and then focus it on the sample with nanometer size by the condenser lens.…”

Section: Discussionmentioning

confidence: 99%

A Compact Ultrafast Electron Diffractometer with Relativistic Femtosecond Electron Pulses

Yang

Gen

Naruse

et al. 2020

QuBS

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We have developed a compact relativistic femtosecond electron diffractometer with a radio-frequency photocathode electron gun and an electron lens system. The electron gun generated 2.5-MeV-energy electron pulses with a duration of 55 ± 5 fs containing 6.3 × 104 electrons per pulse. Using these pulses, we successfully detected high-contrast electron diffraction images of single crystalline, polycrystalline, and amorphous materials. An excellent spatial resolution of diffraction images was obtained as 0.027 ± 0.001 Å−1. In the time-resolved electron diffraction measurement, a laser-excited ultrafast electronically driven phase transition in single-crystalline silicon was observed with a temporal resolution of 100 fs. The results demonstrate the advantages of the compact relativistic femtosecond electron diffractometer, including access to high-order Bragg reflections, single shot imaging with the relativistic femtosecond electron pulse, and the feasibility of time-resolved electron diffraction to study ultrafast structural dynamics.

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Section: Discussionmentioning

confidence: 99%

A Compact Ultrafast Electron Diffractometer with Relativistic Femtosecond Electron Pulses

Yang

Gen

Naruse

et al. 2020

QuBS

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“…Consequently, structure determination often demands more than the combination of XRPD and SSNMR. Over the last decade, 3D electron diffraction (3D ED) has been established as an alternative method for ab initio structure determination of nanometre-sized crystals (Gemmi et al, 2019), including complex zeolites and layered silicates (Mugnaioli & Kolb, 2015;Yun et al, 2015). Based on the development of automated electron diffraction tomography (ADT) (Kolb et al, 2007), it is now possible to sample a substantial fraction of the 3D reciprocal lattice of nanocrystals in a relatively short period of time of less than 1 h. At the same time, the applied electron dose is significantly reduced in comparison with classical zone axis electron diffraction.…”

Section: Introductionmentioning

confidence: 99%

New zeolite-like RUB-5 and its related hydrous layer silicate RUB-6 structurally characterized by electron microscopy

Krysiak

Marler

Barton

et al. 2020

IUCrJ

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This study made use of a recently developed combination of advanced methods to reveal the atomic structure of a disordered nanocrystalline zeolite using exit wave reconstruction, automated diffraction tomography, disorder modelling and diffraction pattern simulation. By applying these methods, it was possible to determine the so far unknown structures of the hydrous layer silicate RUB-6 and the related zeolite-like material RUB-5. The structures of RUB-5 and RUB-6 contain the same dense layer-like building units (LLBUs). In the case of RUB-5, these building units are interconnected via additional SiO4/2 tetrahedra, giving rise to a framework structure with a 2D pore system consisting of intersecting 8-ring channels. In contrast, RUB-6 contains these LLBUs as separate silicate layers terminated by silanol/siloxy groups. Both RUB-6 and RUB-5 show stacking disorder with intergrowths of different polymorphs. The unique structure of RUB-6, together with the possibility for an interlayer expansion reaction to form RUB-5, make it a promising candidate for interlayer expansion with various metal sources to include catalytically active reaction centres.

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“…Crystallography has remained an indispensable method for structure determination since its initial demonstration over a century ago (Bragg & Bragg, 1913). Beyond X-ray diffraction, neutron and electron diffraction have contributed important advances to the crystallographic determination of macromolecular structures (Glaeser, 1999;Shi et al, 2013;Gemmi et al, 2019). Recently, an electron crystallography method called microcrystal electron diffraction (MicroED) has been developed to obtain high-resolution structures from frozen-hydrated three-dimensional macromolecular crystals (Supplementary Fig.…”

Section: Introductionmentioning

confidence: 99%

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

Richards

Millán

Miao

et al. 2020

Acta Cryst Sect D Struct Biol

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Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.

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3D Electron Diffraction: The Nanocrystallography Revolution

Cited by 401 publications

References 176 publications

A Compact Ultrafast Electron Diffractometer with Relativistic Femtosecond Electron Pulses

A Compact Ultrafast Electron Diffractometer with Relativistic Femtosecond Electron Pulses

New zeolite-like RUB-5 and its related hydrous layer silicate RUB-6 structurally characterized by electron microscopy

Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER

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