EMD-30426

Subtomogram averaging
8.7 Å
EMD-30426
3D View Gallery
Deposition: 06/08/2020
Map released: 16/09/2020
Last modified: 11/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links

EMD-30426
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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)
EMICSS annotations (xml)

SARS-CoV-2 prefusion S in RBD down conformation

EMD-30426

Subtomogram averaging
8.7 Å
EMD-30426
3D View Gallery
Deposition: 06/08/2020
Map released: 16/09/2020
Last modified: 11/11/2020
Overview 3D View Sample Experiment Validation Volume Browser Additional data Links
Method: Subtomogram averaging
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 7.5
Grid
Mesh: 300
Model: Quantifoil R2/2
Material: COPPER
Pretreatment
Type: GLOW DISCHARGE
Atmosphere:
Support Film [1]
Material Topology Thickness
CARBON HOLEY -
Vitrification
Cryogen name: ETHANE
Chamber humidity: 100%
Chamber temperature: 20 K
Instrument: GATAN CRYOPLUNGE 3
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: 1.8 µm - 5.0 µm
Calibrated defocus: 1.8 µm - 4.0 µm
Nominal magnification: 64000.0
Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Cooling holder cryogen: NITROGEN
Specialist optics
Energy filter
Name: GIF Quantum LS
Slit width: 20 eV
Image Recording [1]
Detector model: GATAN K3 (6k x 4k)
Detector mode: SUPER-RESOLUTION
Dimensions: 5760 pixel x 4092 pixel
Frames per image: 1-8
Average exposure time: 0.8 s
Average electron dose per image: 3.2 e/Å2
Image processing [1]
Final reconstruction
Resolution: 8.7 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
⌯ Applied Symmetry
Point group: C3
Software [1]
Name Version Details
Dynamo 1.1.333 -
⦩ Final angle assignment
Type: OTHER
Details: Subtomogram averaging
Software [1]
Name Version Details
Dynamo 1.1.333 -
Final 3D classification
Software [1]
Name Version Details
Dynamo 1.1.333 -
Extraction
Number of images used: 25236
Software [1]
Name Version Details
Dynamo 1.1.333 -
CTF correction
Software [2]
Name Version Details
Gctf - -
NOVACTF - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: SARS-CoV-2 prefusion S in RBD down conformation
⬡ Geometry
X Y Z
Dimensions 256 256 256
Origin 0 0 0
Spacing 256 256 256
Voxel size 1.36 Å 1.36 Å 1.36 Å
Contour list
Primary Level Source
True 1.2 AUTHOR