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- EMDB-8799: Yeast 80S ribosome derived from EMPIAR-10045 using emClarity -

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Basic information

Entry
Database: EMDB / ID: 8799
TitleYeast 80S ribosome derived from EMPIAR-10045 using emClarity
Map dataYeast 80S ribosome derived from EMPIAR-10045 using emClarity
SampleS. cerevisiae 80S ribosome:
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsubtomogram averaging / cryo EM / 7.8 Å resolution
AuthorsHimes BA / Zhang P
CitationJournal: Nat. Methods / Year: 2018
Title: emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging.
Authors: Benjamin A Himes / Peijun Zhang
DateDeposition: Jun 30, 2017 / Header (metadata) release: Oct 10, 2018 / Map release: Oct 10, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8799.map.gz (map file in CCP4 format, 121486 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
312 pix
2.17 Å/pix.
= 677.04 Å
312 pix
2.17 Å/pix.
= 677.04 Å
312 pix
2.17 Å/pix.
= 677.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.17 Å
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-15.062231000000001 - 15.681607
Average (Standard dev.)0.010970133 (0.41644982)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions312312312
Origin0.00.00.0
Limit311.0311.0311.0
Spacing312312312
CellA=B=C: 677.04004 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.172.172.17
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z677.040677.040677.040
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-15.06215.6820.011

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Supplemental data

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Mask #1

Fileemd_8799_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Mask #2

Fileemd_8799_msk_2.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire S. cerevisiae 80S ribosome

EntireName: S. cerevisiae 80S ribosome / Details: Non-translating yeast 80s ribosome / Number of components: 1

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Component #1: protein, S. cerevisiae 80S ribosome

ProteinName: S. cerevisiae 80S ribosome / Details: Non-translating yeast 80s ribosome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 53000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000.0 - 5000.0 nm / Energy filter: Gatan Quantum Energy Filter
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 3120
3D reconstructionAlgorithm: BACK PROJECTION / Software: emClarity
CTF correction: Phases were corrected on the projections by multiplication of the astigmatic-CTF determined in emClarity in tiles of 320 sq pix with a strip replacement that depended on the tilt angle.
Resolution: 7.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Independent beyond 3.2 nm as determined by the FSC at the time of dividing the half-sets
Euler angles: 3D refinement with two half-sets fully separated after template matching, at which point the FSC 0.5 was 3.2 nanometers. Reference and subtomograms filtered dynamically according to the FSC at each cycle using the FOM approach.
FSC plot
(resolution estimation)

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