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Cryo-EM structure of SARS-CoV-2 spike protein Ecto-domain with internal tag, All RBD down conformation, State-3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KRR
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.3762 f_angle_d 0.5024 f_chiral_restr 0.0435 f_plane_restr 0.0037 f_bond_d 0.0031
Sample SARS-CoV-2 Spike protein Ectodomain with Internal tag
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 115233 Reported Resolution (Å) 2.7 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7KRR) 2 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 43.97
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 16500 Calibrated Magnification 191780 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION