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- EMDB-25443: CryoEM map of the manually-picked stalled contraction intermediat... -

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Basic information

Entry
Database: EMDB / ID: EMD-25443
TitleCryoEM map of the manually-picked stalled contraction intermediate state of bacteriophage A511.
Map dataCryoEM map of the manually-picked stalled contraction intermediate state of bacteriophage A511.
Sample
  • Virus: Listeria virus A511
Biological speciesListeria virus A511
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsFraser A / Leiman PG
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Identification of Low Population States in Cryo-EM Using Deep Learning
Authors: Fraser A / Prokhorov NS / Miller JM / Knyazhanskaya ES / Leiman PG
History
DepositionNov 17, 2021-
Header (metadata) releaseNov 30, 2022-
Map releaseNov 30, 2022-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25443.png

Downloads & links

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Map

FileDownload / File: emd_25443.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of the manually-picked stalled contraction intermediate state of bacteriophage A511.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.75 Å/pix.
x 600 pix.
= 1650. Å		2.75 Å/pix.
x 600 pix.
= 1650. Å		2.75 Å/pix.
x 600 pix.
= 1650. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-11.373877 - 21.65901
Average (Standard dev.)-7.76897e-10 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 1650.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Listeria virus A511

EntireName: Listeria virus A511
Components
  • Virus: Listeria virus A511

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Supramolecule #1: Listeria virus A511

SupramoleculeName: Listeria virus A511 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 40523 / Sci species name: Listeria virus A511 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 814
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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