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- EMDB-30139: Mature Phage Capsid -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-30139
TitleMature Phage Capsid
Map data
Sample
  • Complex: Mature Phage Capsid
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsChen WY
Funding support1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Protein Cell / Year: 2020
Title: Structural changes of a bacteriophage upon DNA packaging and maturation.
Authors: Wenyuan Chen / Hao Xiao / Xurong Wang / Shuanglin Song / Zhen Han / Xiaowu Li / Fan Yang / Li Wang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
History
DepositionMar 20, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 31, 2021-
Current statusMar 31, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30139.png

Downloads & links

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Map

FileDownload / File: emd_30139.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 540 pix.
= 685.8 Å		1.27 Å/pix.
x 540 pix.
= 685.8 Å		1.27 Å/pix.
x 540 pix.
= 685.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0 / Movie #1: 15
Minimum - Maximum-40.295258 - 90.283356
Average (Standard dev.)-0.104675695 (±8.459662)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-270-270-270
Dimensions540540540
Spacing540540540
CellA=B=C: 685.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z685.800685.800685.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS-270-270-270
NC/NR/NS540540540
D min/max/mean-40.29590.283-0.105

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Supplemental data

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Sample components

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Entire : Mature Phage Capsid

EntireName: Mature Phage Capsid
Components
  • Complex: Mature Phage Capsid

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Supramolecule #1: Mature Phage Capsid

SupramoleculeName: Mature Phage Capsid / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia phage T7 (virus)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)

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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: NITROGEN

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 58690
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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