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A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction.

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Beale EV, Waterman DG, Hecksel C, van Rooyen J, Gilchrist JB, Parkhurst JM, de Haas F, Buijsse B, Evans G, Zhang P
OpenAccess logo Front Mol Biosci 7 179 (2020)
Related entries: 6zeu, 6zev

Cited: 16 times
EuropePMC logo PMID: 32850967

Abstract

MicroED has recently emerged as a powerful method for the analysis of biological structures at atomic resolution. This technique has been largely limited to protein nanocrystals which grow either as needles or plates measuring only a few hundred nanometers in thickness. Furthermore, traditional microED data processing uses established X-ray crystallography software that is not optimized for handling compound effects that are unique to electron diffraction data. Here, we present an integrated workflow for microED, from sample preparation by cryo-focused ion beam milling, through data collection with a standard Ceta-D detector, to data processing using the DIALS software suite, thus enabling routine atomic structure determination of protein crystals of any size and shape using microED. We demonstrate the effectiveness of the workflow by determining the structure of proteinase K to 2.0 Å resolution and show the advantage of using protein crystal lamellae over nanocrystals.

Reviews - 6zet mentioned but not cited (1)

  1. Electron Diffraction of 3D Molecular Crystals. Saha A, Nia SS, Rodríguez JA. Chem Rev 122 13883-13914 (2022)

Articles - 6zet mentioned but not cited (2)

  1. Systemic In Silico Screening in Drug Discovery for Coronavirus Disease (COVID-19) with an Online Interactive Web Server. Xu C, Ke Z, Liu C, Wang Z, Liu D, Zhang L, Wang J, He W, Xu Z, Li Y, Yang Y, Huang Z, Lv P, Wang X, Han D, Li Y, Qiao N, Liu B. J Chem Inf Model 60 5735-5745 (2020)
  2. A Workflow for Protein Structure Determination From Thin Crystal Lamella by Micro-Electron Diffraction. Beale EV, Waterman DG, Hecksel C, van Rooyen J, Gilchrist JB, Parkhurst JM, de Haas F, Buijsse B, Evans G, Zhang P. Front Mol Biosci 7 179 (2020)


Reviews citing this publication (3)

  1. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Gruene T, Mugnaioli E. Chem Rev 121 11823-11834 (2021)
  2. Macromolecular crystallography using microcrystal electron diffraction. Clabbers MTB, Xu H. Acta Crystallogr D Struct Biol 77 313-324 (2021)
  3. MicroED: conception, practice and future opportunities. Clabbers MTB, Shiriaeva A, Gonen T. IUCrJ 9 169-179 (2022)

Articles citing this publication (10)

  1. MicroED structure of lipid-embedded mammalian mitochondrial voltage-dependent anion channel. Martynowycz MW, Khan F, Hattne J, Abramson J, Gonen T. Proc Natl Acad Sci U S A 117 32380-32385 (2020)
  2. MicroED structure of the human adenosine receptor determined from a single nanocrystal in LCP. Martynowycz MW, Shiriaeva A, Ge X, Hattne J, Nannenga BL, Cherezov V, Gonen T. Proc Natl Acad Sci U S A 118 e2106041118 (2021)
  3. Benchmarking the ideal sample thickness in cryo-EM. Martynowycz MW, Clabbers MTB, Unge J, Hattne J, Gonen T. Proc Natl Acad Sci U S A 118 e2108884118 (2021)
  4. Small Molecule Microcrystal Electron Diffraction for the Pharmaceutical Industry-Lessons Learned From Examining Over Fifty Samples. Bruhn JF, Scapin G, Cheng A, Mercado BQ, Waterman DG, Ganesh T, Dallakyan S, Read BN, Nieusma T, Lucier KW, Mayer ML, Chiang NJ, Poweleit N, McGilvray PT, Wilson TS, Mashore M, Hennessy C, Thomson S, Wang B, Potter CS, Carragher B. Front Mol Biosci 8 648603 (2021)
  5. Ab initio phasing macromolecular structures using electron-counted MicroED data. Martynowycz MW, Clabbers MTB, Hattne J, Gonen T. Nat Methods 19 724-729 (2022)
  6. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. Nat Commun 14 1086 (2023)
  7. A simple pressure-assisted method for MicroED specimen preparation. Zhao J, Xu H, Lebrette H, Carroni M, Taberman H, Högbom M, Zou X. Nat Commun 12 5036 (2021)
  8. Protocol for the use of focused ion-beam milling to prepare crystalline lamellae for microcrystal electron diffraction (MicroED). Martynowycz MW, Gonen T. STAR Protoc 2 100686 (2021)
  9. Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals. Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP. Acta Crystallogr D Struct Biol 77 75-85 (2021)
  10. Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae. Parkhurst JM, Crawshaw AD, Siebert CA, Dumoux M, Owen CD, Nunes P, Waterman D, Glen T, Stuart DI, Naismith JH, Evans G. IUCrJ 10 270-287 (2023)


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