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- EMDB-11659: The contracted tail of myophage vb_EcoM_CBA120 (CBA120) -

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Basic information

Entry
Database: EMDB / ID: EMD-11659
TitleThe contracted tail of myophage vb_EcoM_CBA120 (CBA120)
Map dataContracted tail of bacteriophage CBA120
Sample
  • Virus: Escherichia virus CBA120
Biological speciesEscherichia virus CBA120
Methodhelical reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsNazarov S / Leiman P
CitationJournal: To Be Published
Title: Structure of myophage CBA120 from 'Viunalikevirus' genus
Authors: Nazarov S / Taylor N / Leiman P
History
DepositionAug 24, 2020-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateSep 1, 2021-
Current statusSep 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11659.png

Downloads & links

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Map

FileDownload / File: emd_11659.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationContracted tail of bacteriophage CBA120
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.34 Å/pix.
x 256 pix.
= 599.04 Å		2.34 Å/pix.
x 256 pix.
= 599.04 Å		2.34 Å/pix.
x 256 pix.
= 599.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.09140278 - 0.15450834
Average (Standard dev.)-0.00015911409 (±0.011559753)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 599.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.342.342.34
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z599.040599.040599.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0910.155-0.000

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Supplemental data

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Half map: #2

Fileemd_11659_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11659_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia virus CBA120

EntireName: Escherichia virus CBA120
Components
  • Virus: Escherichia virus CBA120

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Supramolecule #1: Escherichia virus CBA120

SupramoleculeName: Escherichia virus CBA120 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1987159 / Sci species name: Escherichia virus CBA120 / 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
Processinghelical reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Component - Name: SM
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 17.566 Å
Applied symmetry - Helical parameters - Δ&Phi: 32.9436 °
Applied symmetry - Helical parameters - Axial symmetry: C6 (6 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 7598
Startup modelType of model: OTHER / Details: Featureless cylinder
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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