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- EMDB-3806: Chloroplast Ribosome, collected with pixel size 1.06 -

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Basic information

Entry
Database: EMDB / ID: 3806
TitleChloroplast Ribosome, collected with pixel size 1.06Chloroplast
Map dataChloroplast
SampleChloroplast ribosome from spinachChloroplast:
SourceSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / 3.2 Å resolution
AuthorsForsberg BO / Aibara S / Kimanius D / Paul B / Lindahl E / Amunts A
CitationJournal: IUCrJ / Year: 2017
Title: Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h.
Authors: Björn O Forsberg / Shintaro Aibara / Dari Kimanius / Bijoya Paul / Erik Lindahl / Alexey Amunts
DateDeposition: Jul 13, 2017 / Header (metadata) release: Aug 23, 2017 / Map release: Nov 1, 2017 / Last update: Nov 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3806.map.gz (map file in CCP4 format, 296353 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
420 pix
1.06 Å/pix.
= 445.2 Å
420 pix
1.06 Å/pix.
= 445.2 Å
420 pix
1.06 Å/pix.
= 445.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.06 (by author), 0.06 (movie #1):
Minimum - Maximum-0.12607083 - 0.30495203
Average (Standard dev.)0.0014280472 (0.012219137)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions420420420
Origin000
Limit419419419
Spacing420420420
CellA=B=C: 445.19998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z445.200445.200445.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1260.3050.001

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Supplemental data

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Mask #1

Fileemd_3806_msk_1.map ( map file in CCP4 format, 296353 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Space group number1

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Mask #1~

Fileemd_3806_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Chloroplast ribosome from spinach

EntireName: Chloroplast ribosome from spinach / Number of components: 1

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Component #1: protein, Chloroplast ribosome from spinach

ProteinName: Chloroplast ribosome from spinachChloroplast / Recombinant expression: No
SourceSpecies: Spinacia oleracea (spinach)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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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: 19 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 / Applied symmetry: C1 (asymmetric) / Number of projections: 100475
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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