|Entry||Database: EMDB / ID: EMD-3808|
|Title||Chloroplast Ribosome, calculated from 20k rescaled particlesChloroplast|
|Sample||Chloroplast ribosome from spinachChloroplast|
|Biological species||Spinacia oleracea (spinach)|
|Method||single particle reconstruction / cryo EM / Resolution: 4.2 Å|
|Authors||Forsberg BO / Aibara S / Kimanius D / Paul B / Lindahl E / Amunts A|
|Citation||Journal: 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 Report||Summary, Full report, XML, About validation report|
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_3808.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.39 Å|
|Symmetry||Space group: 1|
CCP4 map header:
|Projections & Slices|
-Half map: #1
|Projections & Slices|
-Half map: #2
-Entire Chloroplast ribosome from spinach
|Entire||Name: Chloroplast ribosome from spinachChloroplast / Number of components: 1|
-Component #1: protein, Chloroplast ribosome from spinach
|Protein||Name: Chloroplast ribosome from spinachChloroplast / Recombinant expression: No|
|Source||Species: Spinacia oleracea (spinach)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.5|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 19 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 20000|
|3D reconstruction||Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF|
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