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- EMDB-19765: 4D STEM cryo tomogram of t4 Phages produced by iCOM -

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Basic information

Entry
Database: EMDB / ID: EMD-19765
Title4D STEM cryo tomogram of t4 Phages produced by iCOM
Map data4D_STEM cryo tomogram of t4 Phages produced by iCOM
Sample
  • Virus: Escherichia phage T4 (virus)
    • Organelle or cellular component: Escherichia phage T4
Keywords4D STEM cryo tomography / Cryo-ET / CSTET / T4-Phage / iDPC / UNKNOWN FUNCTION
Biological speciesEscherichia phage T4 (virus)
Methodelectron tomography / cryo EM
AuthorsSeifer S / Kirchweger P / Edel KM / Elbaum M
Funding support Austria, Israel, European Union, 4 items
OrganizationGrant numberCountry
Austrian Science FundJ4449-B Austria
Israel Science Foundation1696/18 Israel
European Union (EU)IMpaCT (grant no.857203)European Union
European Research Council (ERC)101055413European Union
CitationJournal: To Be Published
Title: Optimizing contrast in automated 4D-STEM cryo-tomography
Authors: Seifer S / Kirchweger P / Edel KM / Elbaum M
History
DepositionFeb 29, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19765.png

Downloads & links

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Map

FileDownload / File: emd_19765.map.gz / Format: CCP4 / Size: 964 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4D_STEM cryo tomogram of t4 Phages produced by iCOM
Voxel sizeX=Y=Z: 15.58 Å
Density
Minimum - Maximum-2802.627399999999852 - 10775.110000000000582
Average (Standard dev.)2449.13839999999982 (±1387.929100000000062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-895102
Dimensions10241024241
Spacing10241024241
CellA: 15953.92 Å / B: 15953.92 Å / C: 3754.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Escherichia phage T4

EntireName: Escherichia phage T4 (virus)
Components
  • Virus: Escherichia phage T4 (virus)
    • Organelle or cellular component: Escherichia phage T4

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Supramolecule #1: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: virus / ID: 1 / Parent: 0 / Details: Isolated T4 Bacteriophage / NCBI-ID: 2681598 / Sci species name: Escherichia phage T4 / Virus type: VIROID / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Escherichia coli DH5[alpha] (bacteria) / Strain: DH5a

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Supramolecule #2: Escherichia phage T4

SupramoleculeName: Escherichia phage T4 / type: organelle_or_cellular_component / ID: 2 / Parent: 1
Source (natural)Organism: Escherichia phage T4 (virus)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Details: 50 mM Tris pH 8 with 1 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 296.15 K / Instrument: LEICA EM GP
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Home made / Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Calibrated defocus min: 0.0 µm / Illumination mode: SPOT SCAN / Imaging mode: 4D-STEM / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm / Nominal magnification: 41000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Details200 kV with 30 um C2 aperture, for a semi-convergence angle of 0.8 mrad and typically 7-10 pA electron current
Image recordingFilm or detector model: DECTRIS ARINA (0.2k x 0.2k) / Digitization - Dimensions - Width: 1024 pixel / Digitization - Dimensions - Height: 1024 pixel / Average electron dose: 3.0 e/Å2
Details: Images were recorded on a Dectris ARINA 4D-STEM detector.
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION
Software:
Namedetails
MATLAB
PRIISM/IVE (ver. 4.7.2)Deconvolved using core2_decon

Number images used: 41
DetailsThe tilt-images were generated from 4D-STEM data using the iDPC2 algorithm (Seifer et.al., 2024).

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