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- EMDB-7440: 70s ribosome. grids prepared with blot-less method -

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Basic information

Entry
Database: EMDB / ID: EMD-7440
Title70s ribosome. grids prepared with blot-less method
Map datastructure of 70S bacterial ribosome obtained through single particle analyses. The sample has been sprayed on the grid using Surface acoustic waves atomisation
Sample
  • Complex: 70S ribosome from S. aureus
Biological speciesStaphylococcus aureus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
Authorsde Marco A / Ashtiani D / Neild A / Mak J / Venugopal H
CitationJournal: To Be Published
Title: Blot-free grid preparation for cryo-EM: delivery of femtolitre droplets using surface acoustic waves based atomization
Authors: Ashtiani D / Venugopal H / Mak J / Spicer B / Neild A / de Marco A
History
DepositionJan 29, 2018-
Header (metadata) releaseJun 19, 2019-
Map releaseJun 19, 2019-
UpdateJun 19, 2019-
Current statusJun 19, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0245
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7440.png

Downloads & links

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Map

FileDownload / File: emd_7440.map.gz / Format: CCP4 / Size: 184 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of 70S bacterial ribosome obtained through single particle analyses. The sample has been sprayed on the grid using Surface acoustic waves atomisation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 Å		1.3 Å/pix.
x 364 pix.
= 473.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0245 / Movie #1: 0.0245
Minimum - Maximum-0.05270338 - 0.11674303
Average (Standard dev.)0.0008658845 (±0.0052759717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions364364364
Spacing364364364
CellA=B=C: 473.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z364364364
origin x/y/z0.0000.0000.000
length x/y/z473.200473.200473.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ858858858
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS364364364
D min/max/mean-0.0530.1170.001

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Supplemental data

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Sample components

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Entire : 70S ribosome from S. aureus

EntireName: 70S ribosome from S. aureus
Components
  • Complex: 70S ribosome from S. aureus

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Supramolecule #1: 70S ribosome from S. aureus

SupramoleculeName: 70S ribosome from S. aureus / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Staphylococcus aureus (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: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 294 K / Instrument: HOMEMADE PLUNGER
Details: prototype for blotless sample preparation usign SAW atomisation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27409
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: RANDOM ASSIGNMENT

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