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Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VXX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.537 f_angle_d 0.909 f_chiral_restr 0.062 f_bond_d 0.009 f_plane_restr 0.006
Sample SARS-CoV-2 Spike Glycoprotein Ectodomain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 95000 Reported Resolution (Å) 2.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6VXX) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 33.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 3000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.5.6 IMAGE ACQUISITION EPU 2.7 CTF CORRECTION CTFFIND 4.1.10 MODEL FITTING Coot 0.9 FINAL EULER ASSIGNMENT cryoSPARC 2.15 CLASSIFICATION RELION 3.1 RECONSTRUCTION cryoSPARC 2.15 MODEL REFINEMENT PHENIX 1.18
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION