- EMDB-18028: Charging of vitreous samples in cryogenic electron microscopy mit... -
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Entry
Database: EMDB / ID: EMD-18028
Title
Charging of vitreous samples in cryogenic electron microscopy mitigated by graphene - BfrB - Dataset 2 - Quantifoil 300 mesh R1.2/1.3 with Graphene - Small Beam
Map data
Sample
Complex: MYCOBACTERIUM TUBERCULOSIS FERRITIN
Protein or peptide: Ferritin BfrB
Keywords
IRON STORAGE / FERROXIDASE / BACTERIAL FERRITIN / OCTAHEDRAL SYMMETRY. / METAL TRANSPORT / METAL BINDING PROTEIN
Biological species
Mycobacterium tuberculosis H37Rv (bacteria)
Method
single particle reconstruction / cryo EM / Resolution: 2.01 Å
Netherlands Organisation for Scientific Research (NWO)
184.034.014
Netherlands
Health-Holland
LSHM21029
Netherlands
European Commission
815128
European Union
Citation
Journal: ACS Nano / Year: 2023 Title: Charging of Vitreous Samples in Cryogenic Electron Microscopy Mitigated by Graphene. Authors: Yue Zhang / J Paul van Schayck / Adrián Pedrazo-Tardajos / Nathalie Claes / Willem E M Noteborn / Peng-Han Lu / Hans Duimel / Rafal E Dunin-Borkowski / Sara Bals / Peter J Peters / Raimond B G Ravelli / Abstract: Cryogenic electron microscopy can provide high-resolution reconstructions of macromolecules embedded in a thin layer of ice from which atomic models can be built . However, the interaction between ...Cryogenic electron microscopy can provide high-resolution reconstructions of macromolecules embedded in a thin layer of ice from which atomic models can be built . However, the interaction between the ionizing electron beam and the sample results in beam-induced motion and image distortion, which limit the attainable resolutions. Sample charging is one contributing factor of beam-induced motions and image distortions, which is normally alleviated by including part of the supporting conducting film within the beam-exposed region. However, routine data collection schemes avoid strategies whereby the beam is not in contact with the supporting film, whose rationale is not fully understood. Here we characterize electrostatic charging of vitreous samples, both in imaging and in diffraction mode. We mitigate sample charging by depositing a single layer of conductive graphene on top of regular EM grids. We obtained high-resolution single-particle analysis (SPA) reconstructions at 2 Å when the electron beam only irradiates the middle of the hole on graphene-coated grids, using data collection schemes that previously failed to produce sub 3 Å reconstructions without the graphene layer. We also observe that the SPA data obtained with the graphene-coated grids exhibit a higher factor and reduced particle movement compared to data obtained without the graphene layer. This mitigation of charging could have broad implications for various EM techniques, including SPA and cryotomography, and for the study of radiation damage and the development of future sample carriers. Furthermore, it may facilitate the exploration of more dose-efficient, scanning transmission EM based SPA techniques.
Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 6000 pixel / Digitization - Dimensions - Height: 4000 pixel / Number grids imaged: 1 / Number real images: 621 / Average exposure time: 1.7 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 146626
Startup model
Type of model: NONE
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstruction
Applied symmetry - Point group: O (octahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 146626
FSC plot (resolution estimation)
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