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- EMDB-3808: Chloroplast Ribosome, calculated from 20k rescaled particles -

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Basic information

Entry
Database: EMDB / ID: EMD-3808
TitleChloroplast Ribosome, calculated from 20k rescaled particlesChloroplast
Map data
SampleChloroplast ribosome from spinachChloroplast
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
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 /
Abstract: The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on- ...The introduction of direct detectors and the automation of data collection in cryo-EM have led to a surge in data, creating new opportunities for advancing computational processing. In particular, on-the-fly workflows that connect data collection with three-dimensional reconstruction would be valuable for more efficient use of cryo-EM and its application as a sample-screening tool. Here, accelerated on-the-fly analysis is reported with optimized organization of the data-processing tools, image acquisition and particle alignment that make it possible to reconstruct the three-dimensional density of the 70S chlororibosome to 3.2 Å resolution within 24 h of tissue harvesting. It is also shown that it is possible to achieve even faster processing at comparable quality by imposing some limits to data use, as illustrated by a 3.7 Å resolution map that was obtained in only 80 min on a desktop computer. These on-the-fly methods can be employed as an assessment of data quality from small samples and extended to high-throughput approaches.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJul 13, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseNov 1, 2017-
UpdateNov 22, 2017-
Current statusNov 22, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3808.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å
1.39 Å/pix.
x 320 pix.
= 444.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.21863168 - 0.41340804
Average (Standard dev.)0.0019079137 (±0.017089808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 444.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z444.800444.800444.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.2190.4130.002

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Supplemental data

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Segmentation: #1

Fileemd_3808_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_3808_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_3808_half_map_2.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 spinachChloroplast / 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 / Number of projections: 20000
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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