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Structure of the RhGB07 Prefusion, Closed-state trimeric spike protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.1164 f_angle_d 0.517 f_chiral_restr 0.0457 f_plane_restr 0.0028 f_bond_d 0.0016
Sample Trimeric RhGB07 Spike
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 17685 Reported Resolution (Å) 2.97 Resolution Method FSC 0.143 CUT-OFF Other Details Non-Uniform Refinement Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Model was docked using Phenix EMPlace followed by manual building in Coot and phenix real space refine
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 96000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.2+220824 MODEL FITTING PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 3.3.2+220824 FINAL EULER ASSIGNMENT cryoSPARC 3.3.2+220824 RECONSTRUCTION cryoSPARC 3.3.2+220824 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION