EMD-10863

Single-particle
3.3 Å
EMD-10863
3D View Gallery
Deposition: 15/04/2020
Map released: 29/04/2020
Last modified: 02/07/2025
Overview 3D View Sample Experiment Validation Additional data Links
Overview 3D View Sample Experiment Validation Additional data Links

EMD-10863
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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 6yor summary report (pdf.gz) Map and 6yor FULL report (pdf.gz)
EMICSS annotations (xml)

Structure of the SARS-CoV-2 spike S1 protein in complex with CR3022 Fab

EMD-10863

Single-particle
3.3 Å
EMD-10863
3D View Gallery
Deposition: 15/04/2020
Map released: 29/04/2020
Last modified: 02/07/2025
Overview 3D View Sample Experiment Validation Additional data Links
Method: Single-particle
Aggregation State: Particle
Specimen preparation [1]
Buffer
pH: 8.0
Details: 2 mM Tris pH 8.0, 200 mM NaCl, 0.02 % NaN3
Vitrification
Cryogen name: ETHANE
Microscopy [1]
Microscope: FEI TITAN KRIOS
Illumination mode: FLOOD BEAM
Imaging mode: BRIGHT FIELD
Electron source: FIELD EMISSION GUN
Acceleration voltage: 300 kV
Image Recording [1]
Detector model: GATAN K3 (6k x 4k)
Number of grids: 1
Number of real images: 13307
Average exposure time: 1.4 s
Average electron dose per image: 42.0 e/Å2
Image processing [2]
Final reconstruction
Resolution: 3.3 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 327945
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
RELION 3.1 -
Startup model [1]
Type: PDB ENTRY
PDB model: 6VSB
⦨ Initial angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
⦩ Final angle assignment
Type: MAXIMUM LIKELIHOOD
Software [1]
Name Version Details
2.14.1-live -
Particle selection [1]
Selected Ref. model Method Software Details
4852523 - - - Initial from template generated with subset of data.
Final 3D classification
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Details: Default settings in Gctf.
Software [1]
Name Version Details
Gctf 1.06 -
Final reconstruction
Resolution: 3.9 Å ( BY AUTHOR)
Resolution method: FSC 0.143 CUT-OFF
Number of classed used: 1
Number of images used: 100295
Algorithm: BACK PROJECTION
⌯ Applied Symmetry
Point group: C1
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
Startup model [1]
Type: OTHER
Details:RBD-CR3022 map in this deposition.
⦨ Initial angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
⦩ Final angle assignment
Type: ANGULAR RECONSTITUTION
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
Particle selection [1]
Selected Ref. model Method Software Details
4852523 - - - -
Final 3D classification
Software [1]
Name Version Details
CryoSPARC 2.14.1-live -
CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Software [1]
Name Version Details
Gctf - -
Map
Format: CCP4
Data type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation details: The map has strongly anisotropic resolution. RBD and CR3022 Fab are fitted. The S1 N-terminal domains are not well defined and can be viewed at lower contour level, 0.345
⬡ Geometry
X Y Z
Origin 0 0 0
Dimensions (px) 540 540 540
Dimensions (Å) 448.19998 448.19998 448.19998
Voxel size (Å) 0.83 0.83 0.83
Contour list
Primary Level Source
True 0.486 AUTHOR