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- EMDB-30141: Mature Phage t7 core -

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Basic information

Entry
Database: EMDB / ID: EMD-30141
TitleMature Phage t7 core
Map data
SampleMature Phage t7 core
Biological speciesEscherichia phage T7 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsChen WY / Xiao H
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 /
Validation ReportSummary, Full report, XML, About validation report
History
DepositionMar 21, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_30141.map.gz / Format: CCP4 / Size: 125 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 320 pix.
= 406.4 Å
1.27 Å/pix.
x 320 pix.
= 406.4 Å
1.27 Å/pix.
x 320 pix.
= 406.4 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
Contour LevelBy AUTHOR: 7.0 / Movie #1: 3
Minimum - Maximum-4.6791635 - 9.253939
Average (Standard dev.)0.078717895 (±0.7499717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-252-252-252
Dimensions320320320
Spacing320320320
CellA=B=C: 406.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-252-252-252
NC/NR/NS320320320
D min/max/mean-4.6799.2540.079

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Supplemental data

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Sample components

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Entire Mature Phage t7 core

EntireName: Mature Phage t7 core / Number of components: 1

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Component #1: protein, Mature Phage t7 core

ProteinName: Mature Phage t7 core / Recombinant expression: No
SourceSpecies: Escherichia phage T7 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 55212
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

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