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Hogan-Lamarre P, Luo Y, Bücker R, Miller RJD, Zou X. STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials. IUCRJ 2024; 11:62-72. [PMID: 38038991 PMCID: PMC10833385 DOI: 10.1107/s2052252523009661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.
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Affiliation(s)
- Pascal Hogan-Lamarre
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
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2
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Plana-Ruiz S, Gómez-Pérez A, Budayova-Spano M, Foley DL, Portillo-Serra J, Rauch E, Grivas E, Housset D, Das PP, Taheri ML, Nicolopoulos S, Ling WL. High-Resolution Electron Diffraction of Hydrated Protein Crystals at Room Temperature. ACS NANO 2023; 17:24802-24813. [PMID: 37890869 PMCID: PMC10753879 DOI: 10.1021/acsnano.3c05378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Structural characterization is crucial to understanding protein function. Compared with X-ray diffraction methods, electron crystallography can be performed on nanometer-sized crystals and can provide additional information from the resulting Coulomb potential map. Whereas electron crystallography has successfully resolved three-dimensional structures of vitrified protein crystals, its widespread use as a structural biology tool has been limited. One main reason is the fragility of such crystals. Protein crystals can be easily damaged by mechanical stress, change in temperature, or buffer conditions as well as by electron irradiation. This work demonstrates a methodology to preserve these nanocrystals in their natural environment at room temperature for electron diffraction experiments as an alternative to existing cryogenic techniques. Lysozyme crystals in their crystallization solution are hermetically sealed via graphene-coated grids, and their radiation damage is minimized by employing a low-dose data collection strategy in combination with a hybrid-pixel direct electron detector. Diffraction patterns with reflections of up to 3 Å are obtained and successfully indexed using a template-matching algorithm. These results demonstrate the feasibility of in situ protein electron diffraction. The method described will also be applicable to structural studies of hydrated nanocrystals important in many research and technological developments.
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Affiliation(s)
- Sergi Plana-Ruiz
- NanoMegas
SRPL, Rue Emile Claus
49, Brussels 1050, Belgium
- Servei
de Recursos Científics i Tècnics, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
| | | | | | - Daniel L. Foley
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Edgar Rauch
- SIMAP,
Grenoble INP, Université Grenoble Alpes, CNRS, F-38000 Grenoble, France
| | | | | | | | - Mitra L. Taheri
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Wai Li Ling
- Université
Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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3
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Jiang J, Nikbin E, Hicks G, Song S, Liu Y, Wong ECN, Manners I, Howe JY, Winnik MA. Polyferrocenylsilane Block Copolymer Spherulites in Dilute Solution. J Am Chem Soc 2023; 145:1247-1261. [PMID: 36598864 DOI: 10.1021/jacs.2c11119] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Self-assembly of block copolymers (BCP) into uniform 3D structures in solution is an extremely rare phenomenon. Furthermore, the investigation of general prerequisites for fabricating a specific uniform 3D structure remains unknown and challenging. Here, through a simple one-pot direct self-assembly (heating and cooling) protocol, we show that uniform spherulite-like structures and their precursors can be prepared with various poly(ferrocenyldimethylsilane) (PFS) BCPs in a variety of polar and non-polar solvents. These structures all evolve from elongated lamellae into hedrites, sheaf-like micelles, and finally spherulites as the annealing temperature and supersaturation degree are increased. The key feature leading to this growth trajectory is the formation of secondary crystals by self-nucleation on the surface of early-elongated lamellae. We identified general prerequisites for fabricating PFS BCP spherulites in solution. These include corona/PFS core block ratios in the range of 1-5.5 that favor the formation of 2D structures as well as the development of secondary crystals on the basal faces of platelets at early stages of the self-assembly. The one-pot direct self-assembly provides a general protocol to form uniform spherulites and their precursors consisting of PFS BCPs that match these prerequisites. In addition, we show that manipulation of various steps in the direct self-assembly protocol can regulate the size and shape of the structures formed. These general concepts show promise for the fabrication and optimization of spherulites and their precursors from semicrystalline BCPs with interesting optical, electronic, or biomedical properties using the one-pot direct self-assembly protocol.
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Affiliation(s)
- Jingjie Jiang
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ehsan Nikbin
- Department of Material Science and Engineering, University of Toronto, 184 College Street, Toronto, Ontario M5S 3E4, Canada
| | - Garion Hicks
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shaofei Song
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Yang Liu
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Edmond C N Wong
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Ian Manners
- Department of Chemistry, University of Victoria, Victoria, British Columbia V8W 3V6, Canada
| | - Jane Y Howe
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Department of Material Science and Engineering, University of Toronto, 184 College Street, Toronto, Ontario M5S 3E4, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E2, Canada
| | - Mitchell A Winnik
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada.,Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E2, Canada
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Brázda P, Klementová M, Krysiak Y, Palatinus L. Accurate lattice parameters from 3D electron diffraction data. I. Optical distortions. IUCRJ 2022; 9:735-755. [PMID: 36381142 PMCID: PMC9634609 DOI: 10.1107/s2052252522007904] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/05/2022] [Indexed: 05/24/2023]
Abstract
Determination of lattice parameters from 3D electron diffraction (3D ED) data measured in a transmission electron microscope is hampered by a number of effects that seriously limit the achievable accuracy. The distortion of the diffraction patterns by the optical elements of the microscope is often the most severe problem. A thorough analysis of a number of experimental datasets shows that, in addition to the well known distortions, namely barrel-pincushion, spiral and elliptical, an additional distortion, dubbed parabolic, may be observed in the data. In precession electron diffraction data, the parabolic distortion leads to excitation-error-dependent shift and splitting of reflections. All distortions except for the elliptical distortion can be determined together with lattice parameters from a single 3D ED data set. However, the parameters of the elliptical distortion cannot be determined uniquely due to correlations with the lattice parameters. They can be determined and corrected either by making use of the known Laue class of the crystal or by combining data from two or more crystals. The 3D ED data can yield lattice parameter ratios with an accuracy of about 0.1% and angles with an accuracy better than 0.03°.
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Affiliation(s)
- Petr Brázda
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Mariana Klementová
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
| | - Yaşar Krysiak
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
- Institute of Inorganic Chemistry, Leibniz University of Hannover, Callinstraße 9, Hannover, 30167, Germany
| | - Lukáš Palatinus
- Department of Structure Analysis, Institute of Physics of the Czech Academy of Sciences, Na Slovance 1999/2, Prague 8, 18221, Czech Republic
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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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Gruene T, Clabbers MTB, Luebben J, Chin JM, Reithofer MR, Stowasser F, Alker AM. CELLOPT: improved unit-cell parameters for electron diffraction data of small-molecule crystals. J Appl Crystallogr 2022; 55:647-655. [PMID: 35719299 PMCID: PMC9172032 DOI: 10.1107/s160057672200276x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 03/10/2022] [Indexed: 11/12/2022] Open
Abstract
Iterative optimization of the unit-cell parameters improves the refinement of organic small-molecule structures using electron diffraction data. Electron diffraction enables structure determination of organic small molecules using crystals that are too small for conventional X-ray crystallography. However, because of uncertainties in the experimental parameters, notably the detector distance, the unit-cell parameters and the geometry of the structural models are typically less accurate and precise compared with results obtained by X-ray diffraction. Here, an iterative procedure to optimize the unit-cell parameters obtained from electron diffraction using idealized restraints is proposed. The cell optimization routine has been implemented as part of the structure refinement, and a gradual improvement in lattice parameters and data quality is demonstrated. It is shown that cell optimization, optionally combined with geometrical corrections for any apparent detector distortions, benefits refinement of electron diffraction data in small-molecule crystallography and leads to more accurate structural models.
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