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Takaba K, Maki-Yonekura S, Inoue I, Tono K, Fukuda Y, Shiratori Y, Peng Y, Morimoto J, Inoue S, Higashino T, Sando S, Hasegawa T, Yabashi M, Yonekura K. Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds. J Am Chem Soc 2024; 146:5872-5882. [PMID: 38415585 DOI: 10.1021/jacs.3c11523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.
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Affiliation(s)
- Kiyofumi Takaba
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yota Shiratori
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yiying Peng
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Inoue
- Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Toshiki Higashino
- Research Institute for Advanced Electronics and Photonics, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsuo Hasegawa
- Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Koji Yonekura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
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2
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Aizawa H, Sato T, Maki-Yonekura S, Yonekura K, Takaba K, Hamaguchi T, Minato T, Yamamoto HM. Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect. Nat Commun 2023; 14:4530. [PMID: 37507380 PMCID: PMC10382588 DOI: 10.1038/s41467-023-40133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Enantioselectivity of helical aggregation is conventionally directed either by its homochiral ingredients or by introduction of chiral catalysis. The fundamental question, then, is whether helical aggregation that consists only of achiral components can obtain enantioselectivity in the absence of chiral catalysis. Here, by exploiting enantiospecific interaction due to chiral-induced spin selectivity (CISS) that has been known to work to enantio-separate a racemic mixture of chiral molecules, we demonstrate the enantioselectivity in the assembly of mesoscale helical supramolecules consisting of achiral cobalt phthalocyanines. The helical nature in our supramolecules is revealed to be mesoscopically incorporated by dislocation-induced discretized twists, unlike the case of chiral molecules whose chirality are determined microscopically by chemical bond. The relevance of CISS effect in the discretized helical supramolecules is further confirmed by the appearance of spin-polarized current through the system. These observations mean that the application of CISS-based enantioselectivity is no longer limited to systems with microscopic chirality but is expanded to the one with mesoscopic chirality.
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Affiliation(s)
- Hiroki Aizawa
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan
| | - Takuro Sato
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan.
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan.
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Taketoshi Minato
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Hiroshi M Yamamoto
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan.
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan.
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3
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Takaba K, Maki-Yonekura S, Inoue I, Tono K, Hamaguchi T, Kawakami K, Naitow H, Ishikawa T, Yabashi M, Yonekura K. Structural resolution of a small organic molecule by serial X-ray free-electron laser and electron crystallography. Nat Chem 2023; 15:491-497. [PMID: 36941396 PMCID: PMC10719108 DOI: 10.1038/s41557-023-01162-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/16/2023] [Indexed: 03/23/2023]
Abstract
Structure analysis of small crystals is important in areas ranging from synthetic organic chemistry to pharmaceutical and material sciences, as many compounds do not yield large crystals. Here we present the detailed characterization of the structure of an organic molecule, rhodamine-6G, determined at a resolution of 0.82 Å by an X-ray free-electron laser (XFEL). Direct comparison of this structure with that obtained by electron crystallography from the same sample batch of microcrystals shows that both methods can accurately distinguish the position of some of the hydrogen atoms, depending on the type of chemical bond in which they are involved. Variations in the distances measured by XFEL and electron diffraction reflect the expected differences in X-ray and electron scatterings. The reliability for atomic coordinates was found to be better with XFEL, but the electron beam showed a higher sensitivity to charges.
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Affiliation(s)
| | | | | | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Tasuku Hamaguchi
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Aoba-ku, Japan
| | | | | | | | - Makina Yabashi
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan
- Japan Synchrotron Radiation Research Institute, Sayo, Hyogo, Japan
| | - Koji Yonekura
- RIKEN SPring-8 Center, Sayo, Hyogo, Japan.
- Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, Sayo, Hyogo, Japan.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Aoba-ku, Japan.
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4
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Clabbers MTB, Martynowycz MW, Hattne J, Nannenga BL, Gonen T. Electron-counting MicroED data with the K2 and K3 direct electron detectors. J Struct Biol 2022; 214:107886. [PMID: 36044956 PMCID: PMC9999727 DOI: 10.1016/j.jsb.2022.107886] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/19/2022] [Accepted: 08/24/2022] [Indexed: 12/30/2022]
Abstract
Microcrystal electron diffraction (MicroED) uses electron cryo-microscopy (cryo-EM) to collect diffraction data from small crystals during continuous rotation of the sample. As a result of advances in hardware as well as methods development, the data quality has continuously improved over the past decade, to the point where even macromolecular structures can be determined ab initio. Detectors suitable for electron diffraction should ideally have fast readout to record data in movie mode, and high sensitivity at low exposure rates to accurately report the intensities. Direct electron detectors are commonly used in cryo-EM imaging for their sensitivity and speed, but despite their availability are generally not used in diffraction. Primary concerns with diffraction experiments are the dynamic range and coincidence loss, which will corrupt the measurement if the flux exceeds the count rate of the detector. Here, we describe instrument setup and low-exposure MicroED data collection in electron-counting mode using K2 and K3 direct electron detectors and show that the integrated intensities can be effectively used to solve structures of two macromolecules between 1.2 Å and 2.8 Å resolution. Even though a beam stop was not used with the K3 studies we did not observe damage to the camera. As these cameras are already available in many cryo-EM facilities, this provides opportunities for users who do not have access to dedicated facilities for MicroED.
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Affiliation(s)
- Max T B Clabbers
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Arizona State University, Tempe, AZ, United States; Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles CA 90095, United States; Howard Hughes Medical Institute, University of California, Los Angeles CA 90095, United States; Department of Physiology, University of California, Los Angeles CA 90095, United States.
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5
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Abstract
![]()
Electron crystallography
has a storied history which rivals that
of its more established X-ray-enabled counterpart. Recent advances
in data collection and analysis have sparked a renaissance in the
field, opening a new chapter for this venerable technique. Burgeoning
interest in electron crystallography has spawned innovative methods
described by various interchangeable labels (3D ED, MicroED, cRED,
etc.). This Review covers concepts and findings relevant to the practicing
crystallographer, with an emphasis on experiments aimed at using electron
diffraction to elucidate the atomic structure of three-dimensional
molecular crystals.
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Affiliation(s)
- Ambarneil Saha
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Shervin S Nia
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - José A Rodríguez
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States
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6
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Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Ab initio phasing macromolecular structures using electron-counted MicroED data. Nat Methods 2022; 19:724-729. [PMID: 35637302 PMCID: PMC9184278 DOI: 10.1038/s41592-022-01485-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/07/2022] [Indexed: 12/31/2022]
Abstract
Structures of two globular proteins were determined ab initio using microcrystal electron diffraction (MicroED) data that were collected on a direct electron detector in counting mode. Microcrystals were identified using a scanning electron microscope (SEM) and thinned with a focused ion beam (FIB) to produce crystalline lamellae of ideal thickness. Continuous-rotation data were collected using an ultra-low exposure rate to enable electron counting in diffraction. For the first sample, triclinic lysozyme extending to a resolution of 0.87 Å, an ideal helical fragment of only three alanine residues provided initial phases. These phases were improved using density modification, allowing the entire atomic structure to be built automatically. A similar approach was successful on a second macromolecular sample, proteinase K, which is much larger and diffracted to a resolution of 1.5 Å. These results demonstrate that macromolecules can be determined to sub-ångström resolution by MicroED and that ab initio phasing can be successfully applied to counting data.
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Affiliation(s)
- Michael W. Martynowycz
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Max T. B. Clabbers
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Johan Hattne
- grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA USA ,grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, USA. .,Department of Physiology, University of California, Los Angeles, CA, USA.
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7
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Zhou W, Bammes B, Mitchell PG, Betz K, Chiu W. Electron crystallography of chiral and non-chiral small molecules. Ultramicroscopy 2021; 232:113417. [PMID: 34695647 DOI: 10.1016/j.ultramic.2021.113417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/05/2021] [Accepted: 10/16/2021] [Indexed: 11/18/2022]
Abstract
Electron crystallography has recently gained attentions in multiple fields of research, as it has been demonstrated to determine atomic structures for inorganic, organic, and macromolecular materials from nano-sized crystals that were not amenable to conventional X-ray crystallography. Here, we demonstrate continuous-rotation microcrystal electron diffraction (microED) in a 200 kV transmission electron microscope using a DE-64 camera-a low-noise direct electron detector that can accommodate a linear response up to ∼1200 electrons per pixel per second at 20 fps with 2x-hardware-binning, making it ideal for acquisition of high-quality diffraction patterns. We have used this method and camera to determine a 0.75 Å structure of an organic molecule, biotin, with an exceptional goodness-of-fit, as well as a 0.88 Å structure of a chiral molecule, L-serine.
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Affiliation(s)
- Weijiang Zhou
- Biophysics Program, School of Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Kerry Betz
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Bioengineering and Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
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8
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Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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9
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Machine learning-based real-time object locator/evaluator for cryo-EM data collection. Commun Biol 2021; 4:1044. [PMID: 34493805 PMCID: PMC8423793 DOI: 10.1038/s42003-021-02577-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/20/2021] [Indexed: 11/30/2022] Open
Abstract
In cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation. Yonekura et al. present yoneoLocr, a machine learning-based real-time object locator for rapidly and precisely locating carbon holes and crystals for facilitating automated SPA or cryo-EX data collection.
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