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- EMDB-74646: CryoET of tailed phages from partially irrigated soils volume 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-74646
TitleCryoET of tailed phages from partially irrigated soils volume 2
Map data3D reconstructed tomogram of tailed phages at final 8x bin relative to raw data
SampleEnvironmental sample of mixed bacteriophages != unidentified

Environmental sample of mixed bacteriophages

  • Virus: unidentified (others)
Keywordsbacteriophage / soil virus / VIRUS
Biological speciesunidentified (others)
Methodelectron tomography / cryo EM / Resolution: 8.9 Å
AuthorsParvate AD / Alfaro T / McDearis R / Zimmerman A / Nelson WC / Hofmockel KC / Evans JE
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)79415 United States
Department of Energy (DOE, United States)D7G33 United States
CitationJournal: Front Agron / Year: 2026
Title: Cryo-EM visualization of viruses from partially irrigated soils
Authors: Parvate AD / Alfaro T / McDearis R / Zimmerman AE / Hofmockel KS / Nelson WC / Evans JE
History
DepositionDec 21, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74646.png

Downloads & links

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Map

FileDownload / File: emd_74646.map.gz / Format: CCP4 / Size: 905.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstructed tomogram of tailed phages at final 8x bin relative to raw data
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.9 Å/pix.
x 161 pix.
= 1432.9 Å		8.9 Å/pix.
x 1440 pix.
= 12815.999 Å		8.9 Å/pix.
x 1024 pix.
= 9113.6 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: 8.9 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-5.2610497 - 4.6611686
Average (Standard dev.)0.11792222 (±0.3681125)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-9493-13
Dimensions14401024161
Spacing10241440161
CellA: 9113.6 Å / B: 12815.999 Å / C: 1432.8999 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Environmental sample of mixed bacteriophages

EntireName: Environmental sample of mixed bacteriophages
Components
  • Virus: unidentified (others)

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Supramolecule #1: unidentified

SupramoleculeName: unidentified / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 32644 / Sci species name: unidentified / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: unidentified (others)

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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
Details: PPBS: 2% bovine serum albumin, 10% phosphate-buffered saline, 1% potassium citrate, and 150 mM MgSO4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: LEICA EM GP
DetailsSample was polydisperse
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 0.4 sec. / Average electron dose: 1.95 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: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 41000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Software - Name: eTomo / Number images used: 41
CTF correctionSoftware - Name: eTomo
Details: CTF correction during Etomo reconstruction procedure
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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