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- EMDB-42851: 5x5 tiled montage tomogram of a holey carbon grid with apoferriti... -

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Basic information

Entry
Database: EMDB / ID: EMD-42851
Title5x5 tiled montage tomogram of a holey carbon grid with apoferritin imaged with a square electron beam
Map data5x5 tiled montage tomogram of a holey carbon grid with apoferritin imaged with a square electron beam
Sample
  • Complex: Mouse apoferritin at 8 mg/ml, on a carbon foil support
KeywordsIron binding / storage / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsChua EYD / Alink LM / Kopylov M / Johnston J / Einsenstein F / de Marco A
Funding support United States, 2 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Nat Methods / Year: 2024
Title: Square beams for optimal tiling in transmission electron microscopy.
Authors: Eugene Y D Chua / Lambertus M Alink / Mykhailo Kopylov / Jake D Johnston / Fabian Eisenstein / Alex de Marco /
Abstract: Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect ...Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem for dose-sensitive samples. Here, we introduce a square electron beam that can easily be retrofitted in existing microscopes, and demonstrate its application, showing that it can tile nearly perfectly and deliver cryo-electron microscopy imaging with a resolution comparable to conventional set-ups.
History
DepositionNov 16, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42851.png

Downloads & links

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Map

FileDownload / File: emd_42851.map.gz / Format: CCP4 / Size: 11.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation5x5 tiled montage tomogram of a holey carbon grid with apoferritin imaged with a square electron beam
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.04 Å/pix.
x 250 pix.
= 3510. Å		14.04 Å/pix.
x 3586 pix.
= 50347.441 Å		14.04 Å/pix.
x 3410 pix.
= 47876.398 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.04 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 1958670720.0
Average (Standard dev.)592736000.0 (±45810516.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions35863410250
Spacing34103586250
CellA: 47876.4 Å / B: 50347.44 Å / C: 3510.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Mouse apoferritin at 8 mg/ml, on a carbon foil support

EntireName: Mouse apoferritin at 8 mg/ml, on a carbon foil support
Components
  • Complex: Mouse apoferritin at 8 mg/ml, on a carbon foil support

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Supramolecule #1: Mouse apoferritin at 8 mg/ml, on a carbon foil support

SupramoleculeName: Mouse apoferritin at 8 mg/ml, on a carbon foil support
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 460 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.55 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 875

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