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- EMDB-49118: Icosahedral head of Acinetobacter baumannii phage Mystique: empty... -

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Basic information

Entry
Database: EMDB / ID: EMD-49118
TitleIcosahedral head of Acinetobacter baumannii phage Mystique: empty particles only
Map data
Sample
  • Virus: Mystique (virus)
KeywordsMystique / Acinetobacter / phage / bacteriophage / VIRUS
Biological speciesMystique (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.79 Å
AuthorsAlseth EO / Roush C / Irby I / Kopylov M / Bobe D / Diggs M / Nguyen K / Xu H / Schmidt-Krey I / Bryksin AV / Rather PN
Funding support United States, 1 items
OrganizationGrant numberCountry
Simons FoundationSF349247 United States
CitationJournal: To Be Published
Title: Icosahedral head of Acinetobacter baumannii phage Mystique: empty particles only
Authors: Alseth EO / Roush C / Irby I / Kopylov M / Bobe D / Diggs M / Nguyen K / Xu H / Schmidt-Krey I / Bryksin AV / Rather PN
History
DepositionFeb 7, 2025-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49118.png

Downloads & links

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Map

FileDownload / File: emd_49118.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 640 pix.
= 1108.992 Å		1.73 Å/pix.
x 640 pix.
= 1108.992 Å		1.73 Å/pix.
x 640 pix.
= 1108.992 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7328 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.537
Minimum - Maximum-0.31416994 - 1.3392637
Average (Standard dev.)0.0034285786 (±0.12430469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 1108.992 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49118_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: #1

Fileemd_49118_additional_1.map
Projections & Slices
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Half map: #1

Fileemd_49118_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_49118_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Mystique

EntireName: Mystique (virus)
Components
  • Virus: Mystique (virus)

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Supramolecule #1: Mystique

SupramoleculeName: Mystique / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 38018 / Sci species name: Mystique / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acinetobacter baumannii (bacteria) / Strain: AB5075

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.17 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.79 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2793
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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