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SARS-CoV-2-6P-Mut7 S protein (C3 symmetry)
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 10.192 f_angle_d 1.771 f_chiral_restr 0.114 f_bond_d 0.02 f_plane_restr 0.008
Sample SARS-CoV-2 S protein with 6P-Mut7 stabilizing mutations
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 s blot time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 55575 Reported Resolution (Å) 2.8 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 RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 29000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Leginon CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION RELION 3.1 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT Rosetta MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION