EMD-8620

Single-particle
3.8 Å
EMD-8620
3D View Gallery
Deposition: 24/02/2017
Map released: 07/06/2017
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-8620
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3D volume (map.gz) Experimental metadata (xml) Experimental Metadata (cif.gz)
Map-only Validation report (pdf.gz) Map-only Validation report (cif.gz) Map-only Validation report (xml.gz)
Map and PDB model 5uyq summary report (pdf.gz) Map and 5uyq FULL report (pdf.gz)
EMICSS annotations (xml)

70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc)

EMD-8620

Single-particle
3.8 Å
EMD-8620
3D View Gallery
Deposition: 24/02/2017
Map released: 07/06/2017
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Details: 125 nM 50S, 125 nM 30S, 625 nM mRNA, 250 nM fMet-tRNAfMet, 1.25 micromolar EF-Tu, 500 micromolar GDPCP, 1.25 micromolar Lys-tRNALys
Buffer
pH: 7.5
Buffer components [6]:
Name Formula Concentration ChEBI
HEPES - 20.0 mM -
Magnesium chloride MgCl2 20.0 mM
Ammonium chloride NH4Cl 150.0 mM
Spermidine - 2.0 mM -
Spermine - 0.1 mM -
Beta-mercaptoethanol - 6.0 mM -
Grid
Mesh: 400
Model: C-flat-1.2/1.3
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Time: 45 s
Atmosphere: AIR
Support Film [1]
Material Topology Thickness
CARBON HOLEY ARRAY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 90%
Chamber temperature: 275 K
Instrument: GATAN CRYOPLUNGE 3
Details: 2 uL of complex was applied to each grid. After a 10-second incubation, the grids were blotted for 2 to 4 seconds..
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Nominal CS: 2.7 mm
Nominal defocus: 0.5 µm - 5.0 µm
Nominal magnification: 60976.0
Calibrated magnification: 60976.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: COMA FREE
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7676 pixel x 7420 pixel
Frames per image: 1-30
Number of grids: 3
Number of real images: 1773
Average exposure time: 0.4 s
Average electron dose per image: 1.0 e/Å2
Image processing [1]
Details: Gain reference was applied, movies were aligned, and the summed imaged were corrected for magnification anisotropy.
Final reconstruction
Resolution: 3.8 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 3
Number of images used: 5758
Algorithm: BACK PROJECTION
Details:
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
FREALIGN 9.11 -
Startup model [1]
Type: EMDB MAP
EMDB model: EMD-1003
⦨ Initial angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
FREALIGN 9.11 -
⦩ Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
FREALIGN 9.11 -
Particle selection [1]
Selected Ref. model Method Software Details
572417 - - - Particles were picked from micrographs using Signature reference-based particle picker.
Final 3D classification
Number of classes: 6
Avg. number of members per classes: 50000.0
Software [1]
Name Version Details
FREALIGN 9.11 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: 70S ribosome bound with near-cognate ternary complex base-paired to A site codon, closed 30S (Structure III-nc): filtered map from Frealign (FFILT setting in Frealign = T), used for model building after B-factor sharpening. This volume not B-factor sharpened.
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 480 480 480
Dimensions (Å) 393.6 393.6 393.6
Voxel size (Å) 0.82 0.82 0.82
Contour list
Primary Level Source
True 2.85 AUTHOR