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- EMDB-8603: Sub-tomogram average of the archaellar motor in Thermococcus koda... -

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Basic information

Entry
Database: EMDB / ID: 8603
TitleSub-tomogram average of the archaellar motor in Thermococcus kodakaraensis
SampleArchaellar motor
SourceThermococcus kodakaraensis / archaea / thermophilic
Map data
Methodsubtomogram averaging, at 40 Å resolution
AuthorsChang Y-W / Kjaer A / Briegel A / Oikonomou CM / Jensen GJ
CitationEMBO Rep., 2017

EMBO Rep., 2017 StrPapers
Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis.
Ariane Briegel / Catherine M Oikonomou / Yi-Wei Chang / Andreas Kjær / Audrey N Huang / Ki Woo Kim / Debnath Ghosal / Hong H Nguyen / Dorothy Kenny / Rachel R Ogorzalek Loo / Robert P Gunsalus / Grant J Jensen

DateDeposition: Feb 13, 2017 / Header (metadata) release: Feb 22, 2017 / Map release: Jul 26, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.067
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8603.map.gz (map file in CCP4 format, 1001 KB)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
50 pix
6.6 Å/pix.
= 330. Å
100 pix
6.6 Å/pix.
= 660. Å
50 pix
6.6 Å/pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 6.6 Å
Density
Contour Level:0.067 (by author), 0.067 (movie #1):
Minimum - Maximum0.012801021 - 0.1403
Average (Standard dev.)0.05666378 (0.01550041)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions1005050
Origin000
Limit994949
Spacing5010050
CellA: 330 Å / B: 660 Å / C: 330 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.66.66.6
M x/y/z5010050
origin x/y/z0.0000.0000.000
length x/y/z330.000660.000330.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS5010050
D min/max/mean0.0130.1400.057

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Supplemental data

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Sample components

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Entire Archaellar motor

EntireName: Archaellar motor / Number of components: 1

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Component #1: protein, Archaellar motor

ProteinName: Archaellar motor / Recombinant expression: No
SourceSpecies: Thermococcus kodakaraensis / archaea / thermophilic

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C20 (20 fold cyclic)
3D reconstructionSoftware: Tomo3d / Resolution: 40 Å / Resolution method: OTHER

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