Where is crystallography going?

Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.

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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

IUCrJ ◽

10.1107/s205225252000072x ◽

2020 ◽

Vol 7 (2) ◽

pp. 306-323 ◽

Cited By ~ 10

Author(s):

Alexander M. Wolff ◽

Iris D. Young ◽

Raymond G. Sierra ◽

Aaron S. Brewster ◽

Michael W. Martynowycz ◽

...

Keyword(s):

Electron Diffraction ◽

Structural Information ◽

Biological Macromolecules ◽

Structural Studies ◽

Macromolecular Crystallography ◽

Delivery Methods ◽

X Ray ◽

X Ray Crystallography ◽

Physical Conditions ◽

Serial Crystallography

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

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Instrumentation in X-ray crystallography: Past, present and future

Notes and Records the Royal Society journal of the history of science ◽

10.1098/rsnr.2001.0157 ◽

2001 ◽

Vol 55 (3) ◽

pp. 457-472 ◽

Cited By ~ 5

Author(s):

U. W. Arndt

Keyword(s):

Synchrotron Radiation ◽

Three Dimensional ◽

Macromolecular Crystallography ◽

Personal Account ◽

New Techniques ◽

X Ray ◽

X Ray Crystallography ◽

Density Maps ◽

Structure Determinations ◽

Complete Automation

This paper deals with the very great changes in X–ray crystallographic techniques and apparatus over a period of approximately the last 60 years. This is not a general history; it is a personal account of the developments with which I have been directly involved; it is, therefore, biased towards apparatus developments in the field of macromolecular crystallography in which I have worked during most of this period. The bias needs little excuse: many of the new techniques of X–ray crystallography were devised initially for large–molecule structure determinations which had most need of such advances in order to be feasible at all. Among them are the uses of computers in calculating electron density maps, the construction of automatic diffractometers and microdensitometers, the introduction of rotating-anode X–ray generators and of microfocus X–ray tubes, the development of electronic X–ray area detectors, the pioneering work on the use of synchrotron radiation for diffraction studies, the building of three–dimensional atomic models by computer and the complete automation of the mounting, selection and alignment of crystals on the diffractometer.

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Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

10.1101/767061 ◽

2019 ◽

Author(s):

Alexander M Wolff ◽

Iris D Young ◽

Raymond G Sierra ◽

Aaron S Brewster ◽

Michael W Martynowycz ◽

...

Keyword(s):

Electron Diffraction ◽

Structural Information ◽

Biological Macromolecules ◽

Structural Studies ◽

Macromolecular Crystallography ◽

Delivery Methods ◽

X Ray ◽

X Ray Crystallography ◽

Physical Conditions ◽

Serial Crystallography

AbstractInnovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometer to micron scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges not encountered in traditional macromolecular crystallography experiments. Here, we describe XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A (CypA). Our results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample preparation and delivery methods required for each type of experiment effect the crystal structure of the enzyme.

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6. Sources of radiation

Crystallography: A Very Short Introduction ◽

10.1093/actrade/9780198717591.003.0006 ◽

2016 ◽

pp. 107-128

Author(s):

A. M. Glazer

Keyword(s):

Synchrotron Radiation ◽

Electron Diffraction ◽

Visible Light ◽

Free Electron ◽

Horizontal Plane ◽

Vertical Plane ◽

Free Electron Lasers ◽

Neutron Sources ◽

X Ray ◽

Infra Red

To observe diffraction from crystals it is necessary to have a source of radiation whose wavelength is of the same order as the atomic spacings. ‘Sources of radiation’ shows that the electromagnetic spectrum’s X-ray region does this nicely and describes the use of X-ray tubes. Another source of radiation is synchrotron radiation, which exhibits a number of special properties: the radiation emitted ranges from the hard X-ray region, through the ultraviolet and infra-red wavelengths up to visible light; the X-ray beam is plane-polarized within the horizontal plane; and the radiation is highly collimated in the vertical plane. Radiation from free-electron lasers, neutron sources, and electron diffraction is also discussed.

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LB nanotemplate as optimal nanotechnology for synchrotron radiation (SR), cryo-electron microscopy (Cryo-EM) and X-ray free electron lasers (XFELs)

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273316097254 ◽

2016 ◽

Vol 72 (a1) ◽

pp. s185-s185

Author(s):

Eugenia Pechkova ◽

Claudio Nicolini

Keyword(s):

Electron Microscopy ◽

Synchrotron Radiation ◽

Free Electron ◽

Free Electron Lasers ◽

X Ray ◽

Cryo Electron Microscopy

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Electron microscopy of rabbit FC crystals

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100077220 ◽

1983 ◽

Vol 41 ◽

pp. 730-731

Author(s):

Robert A. Grant ◽

Laura L. Degn ◽

Wah Chiu ◽

John Robinson

Keyword(s):

Electron Microscopy ◽

High Resolution ◽

High Resolution Electron Microscopy ◽

Molecular Replacement ◽

X Ray ◽

X Ray Crystallography ◽

Resolution Electron ◽

Replacement Technique ◽

Hydrated Crystal ◽

Molecular Structure Analysis

Proteolytic digestion of the immunoglobulin IgG with papain cleaves the molecule into an antigen binding fragment, Fab, and a compliment binding fragment, Fc. Structures of intact immunoglobulin, Fab and Fc from various sources have been solved by X-ray crystallography. Rabbit Fc can be crystallized as thin platelets suitable for high resolution electron microscopy. The structure of rabbit Fc can be expected to be similar to the known structure of human Fc, making it an ideal specimen for comparing the X-ray and electron crystallographic techniques and for the application of the molecular replacement technique to electron crystallography. Thin protein crystals embedded in ice diffract to high resolution. A low resolution image of a frozen, hydrated crystal can be expected to have a better contrast than a glucose embedded crystal due to the larger density difference between protein and ice compared to protein and glucose. For these reasons we are using an ice embedding technique to prepare the rabbit Fc crystals for molecular structure analysis by electron microscopy.

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Synchrotron Radiation Spectroscopy and Transmission Electron Microscopy Techniques to Evaluate TiO2 NPs Incorporation, Speciation, and Impact on Root Cells Ultrastructure of Pisum sativum L. Plants

Nanomaterials ◽

10.3390/nano11040921 ◽

2021 ◽

Vol 11 (4) ◽

pp. 921

Author(s):

Simonetta Muccifora ◽

Hiram Castillo-Michel ◽

Francesco Barbieri ◽

Lorenza Bellani ◽

Monica Ruffini Castiglione ◽

...

Keyword(s):

Electron Microscopy ◽

Transmission Electron Microscopy ◽

Synchrotron Radiation ◽

Pisum Sativum ◽

Emission Spectrometry ◽

Root Cells ◽

Tio2 Nps ◽

X Ray ◽

Pisum Sativum L ◽

Transmission Electron

Biosolids (Bs) for use in agriculture are an important way for introducing and transferring TiO2 nanoparticles (NPs) to plants and food chain. Roots of Pisum sativum L. plants grown in Bs-amended soils spiked with TiO2 800 mg/kg as rutile NPs, anatase NPs, mixture of both NPs and submicron particles (SMPs) were investigated by Transmission Electron Microscopy (TEM), synchrotron radiation based micro X-ray Fluorescence and micro X-ray Absorption Near-Edge Structure (µXRF/µXANES) and Inductively Coupled Plasma Optical Emission Spectrometry (ICP-OES). TEM analysis showed damages in cells ultrastructure of all treated samples, although a more evident effect was observed with single anatase or rutile NPs treatments. Micro-XRF and TEM evidenced the presence of nano and SMPs mainly in the cortex cells near the rhizodermis. Micro-XRF/micro-XANES analysis revealed anatase, rutile, and ilmenite as the main TiO2 polymorphs in the original soil and Bs, and the preferential anatase uptake by the roots. For all treatments Ti concentration in the roots increased by 38–56%, however plants translocation factor (TF) increased mostly with NPs treatment (261–315%) and less with SMPs (about 85%), with respect to control. In addition, all samples showed a limited transfer of TiO2 to the shoots (very low TF value). These findings evidenced a potential toxicity of TiO2 NPs present in Bs and accumulating in soil, suggesting the necessity of appropriate regulations for the occurrence of NPs in Bs used in agriculture.

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Synthesis and characterization of Fe, Co, and Ni colloids in 2-mercaptoethanol

Nanomaterials and Nanotechnology ◽

10.1177/1847980420966883 ◽

2020 ◽

Vol 10 ◽

pp. 184798042096688

Author(s):

Galo Cárdenas-Triviño ◽

Sergio Triviño-Matus

Keyword(s):

Electron Microscopy ◽

Electron Diffraction ◽

Colloidal Dispersions ◽

Synthesis And Characterization ◽

X Ray ◽

Transmission Electron ◽

Vis Spectroscopy ◽

Chemical Liquid Deposition ◽

Liquid Deposition

Metal colloids in 2-mercaptoethanol using nanoparticles (NPs) of iron (Fe), cobalt (Co), and nickel (Ni) were prepared by chemical liquid deposition method. Transmission electron microscopy, electron diffraction, UV-VIS spectroscopy, and scanning electron microscopy with electron dispersive X-ray spectroscopy characterized the resulting colloidal dispersions. The NPs exhibited sizes with ranges from 9.8 nm for Fe, 3.7 nm for Co, and 7.2 nm for Ni. The electron diffraction shows the presence of the metals in its elemental state Fe (0), Co (0), and Ni (0) and also some compounds FeO (OH), CoCo2S4, and NiNi2S4.

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