EMD-2239

Single-particle
5.57 Å
EMD-2239
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Deposition: 06/12/2012
Map released: 13/02/2013
Last modified: 27/02/2013
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-2239
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3D volume (map.gz) Experimental metadata (xml)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 4v8m summary report (pdf.gz) Map and 4v8m FULL report (pdf.gz)
EMICSS annotations (xml)

Cryo-electron microscopy structure of the Trypanosoma brucei 80S ribosome

EMD-2239

Single-particle
5.57 Å
EMD-2239
3D View Gallery
Deposition: 06/12/2012
Map released: 13/02/2013
Last modified: 27/02/2013
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.105 mg/mL
Buffer
pH: 7.2
Details: 20 mM Tris pH 7.2, 100mM MgCl2, 500 mM KCl, 5 mM beta-mercaptoethanol
Grid
Details: 300 mesh Copper/Molbydenum holey carbon-coated Quantifoil 2/4 grid (Quantifoil Micro Tools GmbH) containing an additional continuous thin layer of carbon
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 100 K
Instrument: FEI VITROBOT MARK IV
Method: Wait 30 sec, Blot 6 seconds, plunge
Microscopy [1]
Microscope: FEI POLARA 300
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.26 mm
Nominal defocus: 1.5 µm - 4.0 µm
Nominal magnification: 59000.0
Specimen holder model: SIDE ENTRY, EUCENTRIC
Image Recording [1]
Detector category: FILM
Detector model: KODAK SO-163 FILM
Scanner: NIKON SUPER COOLSCAN 9000
Number of real images: 1000
Average electron dose per image: 25 e/Å2
Bits per pixel: 32.0
Image processing [1]
Details: Data were processed using SPIDER. The particles windows were automatically extracted from 1000 film-recorded micrographs and inspected manually. Standard SPIDER protocols for reference-based reconstruction, except that contrast transfer function (CTF) of the reconstructions was corrected by phase-flipping the particles using the defocus value estimated for each micrograph and a single reconstruction was obtained from the entire dataset using conjugate gradients with regularization (BP CG in SPIDER).
Final reconstruction
Resolution: 5.57 Å ( BY AUTHOR)
Resolution method: FSC 0.5 CUT-OFF
Number of images used: 164000
Algorithm: OTHER
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
Spider - -
CTF correction
Details:Phase-flip on each particle
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Trypanosoma Brucei 80S Ribosome cryo-em reconstruction filtered according to the local FSC at 0.5
Details: ::::EMDATABANK.org::::EMD-2239::::
⬡ Geometry
X Y Z
Dimensions 359 359 359
Origin -179 -179 -179
Spacing 359 359 359
Voxel size 1.09 Å 1.09 Å 1.09 Å
Contour list
Primary Level Source
True 108000.0 AUTHOR