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1. Advances and applications of microcrystal electron diffraction (MicroED)

   https://doi.org/10.1016/j.sbi.2023.102741  

   Haymaker, Alison; Nannenga, Brent L. (February 2024, Current Opinion in Structural Biology)

   Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography. 

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2. RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences

   https://doi.org/10.1093/nar/gkaa1038  

   Burley, Stephen K; Bhikadiya, Charmi; Bi, Chunxiao; Bittrich, Sebastian; Chen, Li; Crichlow, Gregg V; Christie, Cole H; Dalenberg, Kenneth; Di Costanzo, Luigi; Duarte, Jose M; et al (November 2020, Nucleic Acids Research)

   Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), the US data center for the global PDB archive and a founding member of the Worldwide Protein Data Bank partnership, serves tens of thousands of data depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without restrictions to millions of RCSB.org users around the world, including >660 000 educators, students and members of the curious public using PDB101.RCSB.org. PDB data depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy, 3D electron microscopy and micro-electron diffraction. PDB data consumers accessing our web portals include researchers, educators and students studying fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. During the past 2 years, the research-focused RCSB PDB web portal (RCSB.org) has undergone a complete redesign, enabling improved searching with full Boolean operator logic and more facile access to PDB data integrated with >40 external biodata resources. New features and resources are described in detail using examples that showcase recently released structures of SARS-CoV-2 proteins and host cell proteins relevant to understanding and addressing the COVID-19 global pandemic. 

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3. Focused ion beam milling and MicroED structure determination of metal-organic framework crystals

   https://doi.org/10.1016/j.ultramic.2023.113905  

   Bardin, Andrey A.; Haymaker, Alison; Banihashemi, Fateme; Lin, Jerry Y.S.; Martynowycz, Michael W.; Nannenga, Brent L. (March 2024, Ultramicroscopy)

   We report new advancements in the determination and high-resolution structural analysis of beam-sensitive metal organic frameworks (MOFs) using microcrystal electron diffraction (MicroED) coupled with focused ion beam milling at cryogenic temperatures (cryo-FIB). A microcrystal of the beam-sensitive MOF, ZIF-8, was ion-beam milled in a thin lamella approximately 150 nm thick. MicroED data were collected from this thin lamella using an energy filter and a direct electron detector operating in counting mode. Using this approach, we achieved a greatly improved resolution of 0.59 Å with a minimal total exposure of only 0.64 e−/A2. These innovations not only improve model statistics but also further demonstrate that ion-beam milling is compatible with beam-sensitive materials, augmenting the capabilities of electron diffraction in MOF research. 

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4. Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank

   https://doi.org/10.1093/nar/gkae1091  

   Burley, Stephen K.; Bhatt, Rusham; Bhikadiya, Charmi; Bi, Chunxiao; Biester, Alison; Biswas, Pratyoy; Bittrich, Sebastian; Blaumann, Santiago; Brown, Ronald; Chao, Henry; et al (November 2024, Nucleic Acids Research)

   Abstract The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities. 

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5. Amorphous quininium aspirinate from neat mechanochemistry: diffracting nanocrystalline domains and quick recrystallization upon exposure to solvent vapours

   https://doi.org/10.1039/d5mr00028a  

   Pagola, Silvina; Howard, James; Merkelbach, Johannes; Stam, Danny (April 2025, RSC Mechanochemistry)

   Quininium aspirinate is mechanochemically prepared as a crystalline solid by liquid-assisted grinding, or as an amorphous phase (as determined by X-ray powder diffraction), by neat grinding or neat ball milling. Our previous work demonstrated using FT-IR spectroscopy that a mechanochemical reaction had occurred in the mechanically treated neat mixtures. Herein is reported that microcrystal electron diffraction (microED) afforded the discovery of two diffracting micron-size particles in the amorphous powder synthesized by manual grinding, among a majority of non-diffracting particles. Remarkably, microED data of one of them led to the known lattice parameters of quininium aspirinate. Furthermore, this so-called ‘X-ray amorphous’ phase quickly recrystallizes upon exposure to vapors of N,N-dimethylformamide, or hexane vapours (at a lower rate); but it remains amorphous for longer than 20 months when stored at ambient conditions in a closed container. The lattice parameters and the degrees of crystallinity of both recrystallized materials are identical within the experimental error. However, slightly more intense and better-resolved X-ray powder diffraction peaks are observed in the material recrystallized from N,N-dimethylformamide vapours than in the analogous phase recovered from hexane. As expected, Williamson–Hall graphs lead to a larger average crystalline domain size for the former solid. These results illustrate the use of microED for the investigation of structural features in amorphous phases, and the generic role of the solvent vapours in promoting their recrystallization. 

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