{"entity": "researcher", "timestamp": "2026-08-09T07:21:56.305Z", "family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "affiliations": ["Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, Sweden. hongyi.xu@mmk.su.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8"}}, "publications": [{"entity": "publication", "iuid": "f2d93ddd22d1448f94d015eade7992ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f2d93ddd22d1448f94d015eade7992ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f2d93ddd22d1448f94d015eade7992ac"}}, "title": "Continuous Serial Electron Diffraction for High Quality Protein Structures", "authors": [{"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Wang", "given": "Lei", "initials": "L", "orcid": "0000-0002-7398-1124", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd71b3e4c1b541d8b7f894e7670635f7.json"}}, {"family": "Pacoste", "given": "Laura", "initials": "L", "orcid": "0009-0005-6090-8736", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d78c5b22b984ee5b2803a2bfe8458a3.json"}}, {"family": "Hager", "given": "Paul", "initials": "P", "orcid": "0009-0008-1551-2515", "researcher": {"href": "https://publications.scilifelab.se/researcher/54a85f27eb9b47f48e8fe651912bec02.json"}}, {"family": "Fonjallaz", "given": "Alexis", "initials": "A", "orcid": "0000-0002-9390-1654", "researcher": {"href": "https://publications.scilifelab.se/researcher/e70ff766fd004acd9088745fbefe8c0a.json"}}, {"family": "Williams", "given": "Lewis", "initials": "L", "orcid": "0009-0002-4066-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/2efd72c134204b249eaac0f870e10824.json"}}, {"family": "Scaletti Hutchinson", "given": "Emma", "initials": "E", "orcid": "0000-0002-8741-8981", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a21e353ecb49eba831f7b0d68e024a.json"}}, {"family": "Di Palma", "given": "Michele", "initials": "M", "orcid": "0000-0002-0710-9389", "researcher": {"href": "https://publications.scilifelab.se/researcher/d568035c6a0345c990ee44ab38e85e01.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Worral", "given": "Jonathan", "initials": "J"}, {"family": "Steiner", "given": "Roberto A", "initials": "RA", "orcid": "0000-0001-7084-9745", "researcher": {"href": "https://publications.scilifelab.se/researcher/88121996557f4c0a884e49b720e735cb.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "posted-content", "published": "2025-09-17", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.09.14.676192", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T08:59:49.401Z", "modified": "2025-12-18T19:09:08.443Z"}, {"entity": "publication", "iuid": "245f01038cc64bee8160e4ba13f4a037", "links": {"self": {"href": "https://publications.scilifelab.se/publication/245f01038cc64bee8160e4ba13f4a037.json"}, "display": {"href": "https://publications.scilifelab.se/publication/245f01038cc64bee8160e4ba13f4a037"}}, "title": "Unveiling the Structure of Anhydrous Sodium Valproate with 3D Electron Diffraction and a Facile Sample Preparation Workflow.", "authors": [{"family": "Xu", "given": "Jiaoyan", "initials": "J"}, {"family": "Srinivas", "given": "Vivek", "initials": "V", "orcid": "0000-0002-0265-1873", "researcher": {"href": "https://publications.scilifelab.se/researcher/a6a2692ce1ff4d07ba13f6a180e9232e.json"}}, {"family": "Kumar", "given": "Rohit", "initials": "R"}, {"family": "Pacoste", "given": "Laura", "initials": "L"}, {"family": "Guo", "given": "Yiwang", "initials": "Y"}, {"family": "Yang", "given": "Taimin", "initials": "T", "orcid": "0000-0003-4318-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/1705d217df9c44c98a8be4fa607527fb.json"}}, {"family": "Sun", "given": "Changquan Calvin", "initials": "CC", "orcid": "0000-0001-7284-5334", "researcher": {"href": "https://publications.scilifelab.se/researcher/19052e47349e4a608ec1b11bb1f4388e.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M"}, {"family": "Zou", "given": "Xiaodong", "initials": "X"}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}], "type": "journal article", "published": "2025-06-25", "journal": {"title": "ACS Cent Sci", "issn": "2374-7943", "volume": "11", "issue": "6", "pages": "960-966", "issn-l": null}, "abstract": "Understanding the structure of an active pharmaceutical ingredient is essential for gaining insights into its physicochemical properties. Sodium valproate, one of the most effective antiepileptic drugs, was first approved for medical use in 1967. However, the structure of its anhydrous form has remained unresolved. This is because it was difficult to grow crystals of sufficient size for single-crystal X-ray diffraction (SCXRD). Although 3D electron diffraction (3D ED) can be used for studying crystals that are too small for SCXRD, the crystals of anhydrous sodium valproate are extremely sensitive to both humidity and electron beams. They degrade quickly both in air and under an electron beam at room temperature. In this study, we developed a glovebox-assisted cryo-transfer workflow for the preparation of EM grids in a protected atmosphere to overcome the current challenges for studying air- and beam-sensitive samples using 3D ED. Using this technique, we successfully determined the structure of anhydrous sodium valproate, revealing the formation of Na-valproate polyhedral chains. Our results provide a robust framework for the 3D ED analysis of air-sensitive crystals, greatly enhancing its utility across various scientific disciplines.", "doi": "10.1021/acscentsci.5c00412", "pmid": "40585805", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC12203429"}], "notes": [], "created": "2025-11-25T15:58:49.665Z", "modified": "2025-11-25T15:58:50.127Z"}, {"entity": "publication", "iuid": "6160f0e6036b43428cd4b86676a636f2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6160f0e6036b43428cd4b86676a636f2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6160f0e6036b43428cd4b86676a636f2"}}, "title": "AutoLEI: An XDS-based Graphical User Interface for Automated Real-time and Offline Batch 3D ED/MicroED Data Processing", "authors": [{"family": "Wang", "given": "Lei", "initials": "L", "orcid": "0000-0002-7398-1124", "researcher": {"href": "https://publications.scilifelab.se/researcher/bd71b3e4c1b541d8b7f894e7670635f7.json"}}, {"family": "Chen", "given": "Yinlin", "initials": "Y", "orcid": "0000-0001-7878-2063", "researcher": {"href": "https://publications.scilifelab.se/researcher/7382f35d7b454945a408671eab73efbf.json"}}, {"family": "Hutchinson", "given": "Emma Scaletti", "initials": "ES", "orcid": "0000-0002-8741-8981", "researcher": {"href": "https://publications.scilifelab.se/researcher/34a21e353ecb49eba831f7b0d68e024a.json"}}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "posted-content", "published": "2025-04-12", "journal": {"title": "biorxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2025.04.12.648515", "pmid": null, "labels": {"Cryo-EM": "Service"}, "xrefs": [], "notes": [], "created": "2025-11-26T08:59:34.724Z", "modified": "2025-12-18T19:17:06.658Z"}, {"entity": "publication", "iuid": "dcd91d7cd7a942168973c9bc8e15f009", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dcd91d7cd7a942168973c9bc8e15f009.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dcd91d7cd7a942168973c9bc8e15f009"}}, "title": "A stable zeolite with atomically ordered and interconnected mesopore channel.", "authors": [{"family": "Lu", "given": "Peng", "initials": "P", "orcid": "0000-0002-9773-3993", "researcher": {"href": "https://publications.scilifelab.se/researcher/f3854822aeed43b9965d2641f05f4afe.json"}}, {"family": "Xu", "given": "Jiaoyan", "initials": "J"}, {"family": "Sun", "given": "Yiqing", "initials": "Y"}, {"family": "Guillet-Nicolas", "given": "R\u00e9my", "initials": "R"}, {"family": "Willhammar", "given": "Tom", "initials": "T", "orcid": "0000-0001-6120-1218", "researcher": {"href": "https://publications.scilifelab.se/researcher/2eba775271684de1a7d19673ae79a7f7.json"}}, {"family": "Fahda", "given": "Mohammad", "initials": "M", "orcid": "0000-0003-4087-1022", "researcher": {"href": "https://publications.scilifelab.se/researcher/0ae92159698b457a98a24097dc25e48d.json"}}, {"family": "Dib", "given": "Eddy", "initials": "E", "orcid": "0000-0001-6062-3128", "researcher": {"href": "https://publications.scilifelab.se/researcher/7dd020645988424bb5565a7be7773a1e.json"}}, {"family": "Wang", "given": "Bo", "initials": "B"}, {"family": "Qin", "given": "Zhengxing", "initials": "Z"}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Cho", "given": "Jung", "initials": "J", "orcid": "0009-0009-9519-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/14fc3928337344b38e5485c9589d802a.json"}}, {"family": "Liu", "given": "Zhaopeng", "initials": "Z"}, {"family": "Yu", "given": "Haijun", "initials": "H"}, {"family": "Yang", "given": "Xiaobo", "initials": "X", "orcid": "0000-0001-9373-8685", "researcher": {"href": "https://publications.scilifelab.se/researcher/388766fc3db244eab6cdae48c9b6cf67.json"}}, {"family": "Lang", "given": "Qiaolin", "initials": "Q"}, {"family": "Mintova", "given": "Svetlana", "initials": "S", "orcid": "0000-0002-0738-5244", "researcher": {"href": "https://publications.scilifelab.se/researcher/c358cafcab81469c8262c2d9ebdfcf12.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}, {"family": "Valtchev", "given": "Valentin", "initials": "V", "orcid": "0000-0002-2341-6397", "researcher": {"href": "https://publications.scilifelab.se/researcher/5565c2d06de34c9f95a1db510647347c.json"}}], "type": "journal article", "published": "2024-12-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "636", "issue": "8042", "pages": "368-373", "issn-l": "0028-0836"}, "abstract": "Zeolites are crystalline microporous materials constructed by corner-sharing tetrahedra (SiO4 and AlO4), with many industrial applications as ion exchangers, adsorbents and heterogeneous catalysts1-4. However, the presence of micropores impedes the use of zeolites in areas dealing with bulky substrates. Introducing extrinsic mesopores, that is, intercrystal/intracrystal mesopores, in zeolites is a solution to overcome the diffusion barrier5-8. Still, those extrinsic mesopores are generally disordered and non-uniform; moreover, acidity and crystallinity are always, to some extent, impaired9. Thus, synthesizing thermally stable zeolites with intrinsic mesopores that are of uniform size and crystallographically connected with micropores, denoted here as intrinsic mesoporous zeolite, is highly desired but still not achieved. Here we report ZMQ-1 (Zeolitic Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, no. 1), an aluminosilicate zeolite with an intersecting intrinsic meso-microporous channel system delimited by 28 \u00d7 10 \u00d7 10-rings, in which the 28-ring has a free diameter of 22.76 \u00c5 \u00d7 11.83 \u00c5, which reaches the mesopore domain. ZMQ-1 has high thermal and hydrothermal stability with tunable framework Si/Al molar ratios. ZMQ-1 is the first aluminosilicate zeolite with an intrinsic meso-microporous channel system. The Br\u00f8nsted acidity of ZMQ-1 imparts high activity and unique selectivity in the catalytic cracking of heavy oil. The position of the organic structure-directing agent (OSDA) used for ZMQ-1 synthesis was determined from three-dimensional electron diffraction (3D ED) data, which shows the unique structure-directing role of the OSDA in the formation of the intrinsic meso-microporous zeolite. This provides an incentive for preparing other stable mesopore-containing zeolites.", "doi": "10.1038/s41586-024-08206-1", "pmid": "39663489", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11634760"}, {"db": "pii", "key": "10.1038/s41586-024-08206-1"}], "notes": [], "created": "2025-11-26T08:59:01.854Z", "modified": "2025-11-26T08:59:03.012Z"}, {"entity": "publication", "iuid": "a5edd32e34ca4d70895006cf2d3f8d72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5edd32e34ca4d70895006cf2d3f8d72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5edd32e34ca4d70895006cf2d3f8d72"}}, "title": "Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.", "authors": [{"family": "Li", "given": "Y", "initials": "Y", "orcid": "0000-0001-8317-824X", "researcher": {"href": "https://publications.scilifelab.se/researcher/19c182a9efbd438787c46812f3e0bd98.json"}}, {"family": "Pacoste", "given": "L C", "initials": "LC", "orcid": "0009-0005-6090-8736", "researcher": {"href": "https://publications.scilifelab.se/researcher/1d78c5b22b984ee5b2803a2bfe8458a3.json"}}, {"family": "Gu", "given": "W", "initials": "W", "orcid": "0000-0002-1185-3557", "researcher": {"href": "https://publications.scilifelab.se/researcher/19785d2333584427b5211b7cc60867bb.json"}}, {"family": "Thygesen", "given": "S J", "initials": "SJ", "orcid": "0000-0002-7512-4097", "researcher": {"href": "https://publications.scilifelab.se/researcher/e41f6ad37780455983f73db785903907.json"}}, {"family": "Stacey", "given": "K J", "initials": "KJ", "orcid": "0000-0002-3992-7802", "researcher": {"href": "https://publications.scilifelab.se/researcher/af54c84a4bf34673be1efdecbcf701dd.json"}}, {"family": "Ve", "given": "T", "initials": "T", "orcid": "0000-0002-0113-1905", "researcher": {"href": "https://publications.scilifelab.se/researcher/654d5a7904694d2dbeb00f4dc718fe99.json"}}, {"family": "Kobe", "given": "B", "initials": "B", "orcid": "0000-0001-9413-9166", "researcher": {"href": "https://publications.scilifelab.se/researcher/b7de23cf90764ba5a38892c47ca042cc.json"}}, {"family": "Xu", "given": "H", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Nanson", "given": "J D", "initials": "JD", "orcid": "0000-0003-1306-1948", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee17f582fbf049118c7e4709fdbff822.json"}}], "type": "journal article", "published": "2024-09-01", "journal": {"title": "Acta Crystallogr D Struct Biol", "issn": "2059-7983", "volume": "80", "issue": "Pt 9", "pages": "699-712", "issn-l": "2059-7983"}, "abstract": "Eukaryotic TIR (Toll/interleukin-1 receptor protein) domains signal via TIR-TIR interactions, either by self-association or by interaction with other TIR domains. In mammals, TIR domains are found in Toll-like receptors (TLRs) and cytoplasmic adaptor proteins involved in pro-inflammatory signaling. Previous work revealed that the MAL TIR domain (MALTIR) nucleates the assembly of MyD88TIR into crystalline arrays in vitro. A microcrystal electron diffraction (MicroED) structure of the MyD88TIR assembly has previously been solved, revealing a two-stranded higher-order assembly of TIR domains. In this work, it is demonstrated that the TIR domain of TLR2, which is reported to signal as a heterodimer with either TLR1 or TLR6, induces the formation of crystalline higher-order assemblies of MyD88TIR in vitro, whereas TLR1TIR and TLR6TIR do not. Using an improved data-collection protocol, the MicroED structure of TLR2TIR-induced MyD88TIR microcrystals was determined at a higher resolution (2.85 \u00c5) and with higher completeness (89%) compared with the previous structure of the MALTIR-induced MyD88TIR assembly. Both assemblies exhibit conformational differences in several areas that are important for signaling (for example the BB loop and CD loop) compared with their monomeric structures. These data suggest that TLR2TIR and MALTIR interact with MyD88 in an analogous manner during signaling, nucleating MyD88TIR assemblies unidirectionally.", "doi": "10.1107/S2059798324008210", "pmid": "39268708", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11394124"}, {"db": "pii", "key": "S2059798324008210"}], "notes": [], "created": "2024-11-15T13:42:00.132Z", "modified": "2024-11-15T13:42:00.492Z"}, {"entity": "publication", "iuid": "5522dfaad4c24860b50669a2aa99cec9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5522dfaad4c24860b50669a2aa99cec9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5522dfaad4c24860b50669a2aa99cec9"}}, "title": "Accurate structure models and absolute configuration determination using dynamical effects in continuous-rotation 3D electron diffraction data.", "authors": [{"family": "Klar", "given": "Paul B", "initials": "PB", "orcid": "0000-0002-1625-5353", "researcher": {"href": "https://publications.scilifelab.se/researcher/037931c9b2df4fc8bb0add690654dd0a.json"}}, {"family": "Krysiak", "given": "Ya\u015far", "initials": "Y", "orcid": "0000-0001-9314-8394", "researcher": {"href": "https://publications.scilifelab.se/researcher/140c8ea270414797ae59ee0fe26c149d.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Steciuk", "given": "Gwladys", "initials": "G"}, {"family": "Cho", "given": "Jung", "initials": "J"}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}, {"family": "Palatinus", "given": "Lukas", "initials": "L", "orcid": "0000-0002-8987-8164", "researcher": {"href": "https://publications.scilifelab.se/researcher/eba67300cdf94ea0905989243614d6f4.json"}}], "type": "journal article", "published": "2023-06-00", "journal": {"title": "Nat Chem", "issn": "1755-4349", "volume": "15", "issue": "6", "pages": "848-855", "issn-l": null}, "abstract": "Continuous-rotation 3D electron diffraction methods are increasingly popular for the structure analysis of very small organic molecular crystals and crystalline inorganic materials. Dynamical diffraction effects cause non-linear deviations from kinematical intensities that present issues in structure analysis. Here, a method for structure analysis of continuous-rotation 3D electron diffraction data is presented that takes multiple scattering effects into account. Dynamical and kinematical refinements of 12 compounds-ranging from small organic compounds to metal-organic frameworks to inorganic materials-are compared, for which the new approach yields significantly improved models in terms of accuracy and reliability with up to fourfold reduction of the noise level in difference Fourier maps. The intrinsic sensitivity of dynamical diffraction to the absolute structure is also used to assign the handedness of 58 crystals of 9 different chiral compounds, showing that 3D electron diffraction is a reliable tool for the routine determination of absolute structures.", "doi": "10.1038/s41557-023-01186-1", "pmid": "37081207", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10239730"}, {"db": "pii", "key": "10.1038/s41557-023-01186-1"}], "notes": [], "created": "2023-11-26T08:57:06.221Z", "modified": "2023-11-26T08:57:06.337Z"}, {"entity": "publication", "iuid": "ada46154eb9a49bb9d99d76e1331e845", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ada46154eb9a49bb9d99d76e1331e845.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ada46154eb9a49bb9d99d76e1331e845"}}, "title": "Phase identification and discovery of hidden crystal forms in a polycrystalline pharmaceutical sample using high-throughput 3D electron diffraction", "authors": [{"family": "Lightowler", "given": "Molly", "initials": "M"}, {"family": "Li", "given": "Shuting", "initials": "S"}, {"family": "Ou", "given": "Xiao", "initials": "X"}, {"family": "Cho", "given": "Jungyoun", "initials": "J", "orcid": "0009-0009-9519-2992", "researcher": {"href": "https://publications.scilifelab.se/researcher/14fc3928337344b38e5485c9589d802a.json"}}, {"family": "Li", "given": "Ao", "initials": "A"}, {"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Xu", "given": "Jiaoyan", "initials": "J"}, {"family": "Yang", "given": "Taimin", "initials": "T", "orcid": "0000-0003-4318-8990", "researcher": {"href": "https://publications.scilifelab.se/researcher/1705d217df9c44c98a8be4fa607527fb.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}, {"family": "Lu", "given": "Ming", "initials": "M", "orcid": "0000-0002-2622-1528", "researcher": {"href": "https://publications.scilifelab.se/researcher/58720a90d228470aa5fb7478a68c9cdd.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}], "type": "posted-content", "published": "2023-05-19", "journal": {"title": "chemrxiv", "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.26434/chemrxiv-2023-2rh9j", "pmid": null, "labels": {"Cryo-EM": "Technology development"}, "xrefs": [], "notes": [], "created": "2023-11-26T14:19:54.671Z", "modified": "2025-12-18T19:51:15.742Z"}, {"entity": "publication", "iuid": "af513f133ef440dc9dc4e8c91d5a967a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/af513f133ef440dc9dc4e8c91d5a967a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/af513f133ef440dc9dc4e8c91d5a967a"}}, "title": "Direct structure determination of vemurafenib polymorphism from compact spherulites using 3D electron diffraction.", "authors": [{"family": "Li", "given": "Shuting", "initials": "S"}, {"family": "Lightowler", "given": "Molly", "initials": "M"}, {"family": "Ou", "given": "Xiao", "initials": "X"}, {"family": "Huang", "given": "Siyong", "initials": "S"}, {"family": "Jiang", "given": "Yifan", "initials": "Y"}, {"family": "Li", "given": "Xizhen", "initials": "X"}, {"family": "Zou", "given": "Xiaodong", "initials": "X"}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Lu", "given": "Ming", "initials": "M", "orcid": "0000-0002-2622-1528", "researcher": {"href": "https://publications.scilifelab.se/researcher/58720a90d228470aa5fb7478a68c9cdd.json"}}], "type": "journal article", "published": "2023-01-23", "journal": {"title": "Commun Chem", "issn": "2399-3669", "volume": "6", "issue": "1", "pages": "18", "issn-l": null}, "abstract": "The spherulitic morphology is considered to be the most common morphology of crystalline materials and is particularly apparent in melt-crystallized products. Yet, historically, the polycrystalline nature of spherulites has hindered successful crystal structure determination. Here, we report the direct structure determination of a clinical drug, vemurafenib (VMN), in compact spherulite form using 3D electron diffraction (3D ED). VMN has four known polymorphs. We first solved the crystal structures of \u03b1-, \u03b2-, and \u03b3-VMN from compact spherulites using 3D ED, and the resulting structures were highly consistent with those obtained by single-crystal X-ray diffraction. We then determined the crystal structure of \u03b4-VMN-the least stable polymorph which cannot be cultivated as a single crystal-directly from the compact spherulite sample. We unexpectedly discovered a new polymorph during our studies, denoted as \u03b5-VMN. Single crystals of \u03b5-VMN are extremely thin and not suitable for study by X-ray diffraction. Again, we determined the structure of \u03b5-VMN in a compact spherulite form. This successful structure elucidation of all five VMN polymorphs demonstrates the possibility of directly determining structures from melt-grown compact spherulite samples. Thereby, this discovery will improve the efficiency and broaden the scope of polymorphism research, especially within the field of melt crystallization.", "doi": "10.1038/s42004-022-00804-2", "pmid": "36697943", "labels": {"Cryo-EM": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC9871043"}, {"db": "pii", "key": "10.1038/s42004-022-00804-2"}], "notes": [], "created": "2023-11-26T08:57:53.371Z", "modified": "2023-11-26T08:57:53.412Z"}, {"entity": "publication", "iuid": "7300ff993bda42d4b56a54b1f754c336", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7300ff993bda42d4b56a54b1f754c336.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7300ff993bda42d4b56a54b1f754c336"}}, "title": "Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data.", "authors": [{"family": "Bengtsson", "given": "Viktor E G", "initials": "VEG", "orcid": "0000-0002-6020-9178", "researcher": {"href": "https://publications.scilifelab.se/researcher/5e42c1186004482fb7c997ac7e05320f.json"}}, {"family": "Pacoste", "given": "Laura", "initials": "L", "orcid": "0000-0002-9931-2682", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda39f6d0e9a4261b75297992b0faa2d.json"}}, {"family": "de la Rosa-Trevin", "given": "Jos\u00e9 Miguel", "initials": "JM", "orcid": "0000-0002-3320-1269", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9c797d9907249f0bb608c1340ac6f5c.json"}}, {"family": "Hofer", "given": "Gerhard", "initials": "G", "orcid": "0000-0002-9248-6989", "researcher": {"href": "https://publications.scilifelab.se/researcher/5fcf436f51b14189b0c6668e6903afd8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}], "type": "journal article", "published": "2022-06-01", "journal": {"title": "J Appl Crystallogr", "issn": "1600-5767", "issn-l": null, "volume": "55", "issue": "Pt 3", "pages": "638-646"}, "abstract": "Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.", "doi": "10.1107/S1600576722002758", "pmid": "35719296", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC9172039"}, {"db": "pii", "key": "S1600576722002758"}], "notes": [], "created": "2022-04-29T08:05:20.733Z", "modified": "2024-01-19T12:43:19.351Z"}, {"entity": "publication", "iuid": "6c9beebec3bf4e008aa3f11261cfa6e6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c9beebec3bf4e008aa3f11261cfa6e6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c9beebec3bf4e008aa3f11261cfa6e6"}}, "title": "A simple pressure-assisted method for MicroED specimen preparation.", "authors": [{"family": "Zhao", "given": "Jingjing", "initials": "J", "orcid": "0000-0001-8444-6883", "researcher": {"href": "https://publications.scilifelab.se/researcher/3fbe7f2ca29941ce98c38ca6bf78c534.json"}}, {"family": "Xu", "given": "Hongyi", "initials": "H", "orcid": "0000-0002-8271-3906", "researcher": {"href": "https://publications.scilifelab.se/researcher/f112e6110df1446bbfb2679518da45d8.json"}}, {"family": "Lebrette", "given": "Hugo", "initials": "H", "orcid": "0000-0002-8081-181X", "researcher": {"href": "https://publications.scilifelab.se/researcher/17ace145c59b4e8695a5c9b95fe81b92.json"}}, {"family": "Carroni", "given": "Marta", "initials": "M", "orcid": "0000-0002-7697-6427", "researcher": {"href": "https://publications.scilifelab.se/researcher/e7f1bc1767024368abcb11a83184994a.json"}}, {"family": "Taberman", "given": "Helena", "initials": "H"}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications.scilifelab.se/researcher/d968fcccace74b689185bb9fa2d33bf8.json"}}, {"family": "Zou", "given": "Xiaodong", "initials": "X", "orcid": "0000-0001-6748-6656", "researcher": {"href": "https://publications.scilifelab.se/researcher/b9bd566204e3499db43d53f2adf626e0.json"}}], "type": "journal article", "published": "2021-08-19", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "12", "issue": "1", "pages": "5036", "issn-l": "2041-1723"}, "abstract": "Micro-crystal electron diffraction (MicroED) has shown great potential for structure determination of macromolecular crystals too small for X-ray diffraction. However, specimen preparation remains a major bottleneck. Here, we report a simple method for preparing MicroED specimens, named Preassis, in which excess liquid is removed through an EM grid with the assistance of pressure. We show the ice thicknesses can be controlled by tuning the pressure in combination with EM grids with appropriate carbon hole sizes. Importantly, Preassis can handle a wide range of protein crystals grown in various buffer conditions including those with high viscosity, as well as samples with low crystal concentrations. Preassis is a simple and universal method for MicroED specimen preparation, and will significantly broaden the applications of MicroED.", "doi": "10.1038/s41467-021-25335-7", "pmid": "34413316", "labels": {"Cryo-EM": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-021-25335-7"}, {"db": "pmc", "key": "PMC8377027"}], "notes": [], "created": "2021-12-14T12:47:04.167Z", "modified": "2023-12-04T10:18:11.258Z"}]}