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- EMDB-8592: Subtomogram average of microtubules from PC12 cell -

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Basic information

Entry
Database: EMDB / ID: 8592
TitleSubtomogram average of microtubules from PC12 cell
SampleMicrotubule from PC12 cells
SourceRattus / mammal / image: Rattus norvegicus
Map data
Methodsubtomogram averaging, at 64 Å resolution
AuthorsChen M / Dai W / Schmid MF / Chiu W / Ludtke SJ
CitationNat. Methods, 2017

Nat. Methods, 2017 StrPapers
Convolutional neural networks for automated annotation of cellular cryo-electron tomograms.
Muyuan Chen / Wei Dai / Stella Y Sun / Darius Jonasch / Cynthia Y He / Michael F Schmid / Wah Chiu / Steven J Ludtke

DateDeposition: Feb 3, 2017 / Header (metadata) release: Mar 1, 2017 / Map release: Mar 1, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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  • Surface view colored by cylindrical radius
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
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Supplemental images

emd_8592.png

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Map

Fileemd_8592.map.gz (map file in CCP4 format, 443 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
48 pix
14.3 Å/pix.
= 686.4 Å		48 pix
14.3 Å/pix.
= 686.4 Å		48 pix
14.3 Å/pix.
= 686.4 Å

Surface

Projections

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Images are generated by Spider package.

Voxel sizeX=Y=Z: 14.3 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-1.6776736 - 1.7911501
Average (Standard dev.)-0.0029733914 (0.28868338)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions484848
Origin-24-24-24
Limit232323
Spacing484848
CellA=B=C: 686.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.314.314.3
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z686.400686.400686.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-1.6781.791-0.003

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Supplemental data

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Sample components

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Entire Microtubule from PC12 cells

EntireName: Microtubule from PC12 cells / Number of components: 1

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Component #1: cellular-component, Microtubule from PC12 cells

Cellular-componentName: Microtubule from PC12 cells / Recombinant expression: No
SourceSpecies: Rattus / mammal / image: Rattus norvegicus
Source (natural)Organ or tissue: adrenal medulla

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Experimental details

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Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2100
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: BACK PROJECTION / Software: EMAN / Resolution: 64 Å / Resolution method: FSC 0.143 CUT-OFF

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