EMD-8473

Single-particle
5.1 Å
EMD-8473
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Deposition: 22/11/2016
Map released: 21/12/2016
Last modified: 13/03/2024
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Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-8473
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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)
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EMICSS annotations (xml)

Architecture of the yeast small subunit processome

EMD-8473

Single-particle
5.1 Å
EMD-8473
3D View Gallery
Deposition: 22/11/2016
Map released: 21/12/2016
Last modified: 13/03/2024
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Concentration: 0.15 mg/mL
Buffer
pH: 7.7
Buffer components [5]:
Name Formula Concentration ChEBI
Sodium chloride NaCl 150.0 mM
Tris (HOCH2)3CNH2 50.0 mM
EDTA - 1.0 mM -
Biotin - 5.0 mM -
Triton X-100 - 0.03 % -
Grid
Mesh: 400
Model: Ted Pella Inc.
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Time: {'units': 's', 'valueOf_': '30'}
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON LACEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 295 K
Instrument: FEI VITROBOT MARK IV
Details: Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing..
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
C2 aperture diameter: 70.0 µm
Nominal CS: 2.7 mm
Nominal defocus: 0.6 µm - 2.6 µm
Nominal magnification: 22500.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Alignment procedure: BASIC
Temperature
Minimum: 78.0 K
Maximum: 80.0 K
Image Recording [1]
Detector model: GATAN K2 SUMMIT (4k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 7420 pixel x 7676 pixel
Frames per image: 3-16
Number of grids: 1
Number of real images: 1714
Average exposure time: 0.25 s
Average electron dose per image: 1.56 e/Å2
Image processing [1]
Final reconstruction
Resolution: 5.1 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 2
Number of images used: 33813
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 2 -
Startup model [1]
Type: INSILICO MODEL
Insilico model: Generated from negative stain
⦨ Initial angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
RELION 2 -
⦩ Final angle assignment
Type: RANDOM ASSIGNMENT
Software [1]
Name Version Details
RELION 2 -
Particle selection [1]
Selected Ref. model Method Software Details
79414 - - - -
Final 3D classification
Number of classes: 5
Software [1]
Name Version Details
RELION 2 -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: Yeast small subunit processome
⬡ Geometry
X Y Z
Dimensions 380 380 380
Origin 0 0 0
Spacing 380 380 380
Voxel size 1.325 Å 1.325 Å 1.325 Å
Contour list
Primary Level Source
True 0.018 AUTHOR