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SARS-CoV-2 Spike (dimers) in complex with six Fu2 nanobodies
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KSG
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.67 f_angle_d 0.823 f_chiral_restr 0.062 f_plane_restr 0.005 f_bond_d 0.004
Sample Spike RBD (two molecules) in complex with two FU2 nanobodies Sample Components Fu2 nanobody SARS-CoV-2 Spike, Fibritin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 277372 Reported Resolution (Å) 3.18 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7KSG) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 48.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 300 Maximum Defocus (nm) 2500 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU 2.7 CTF CORRECTION Warp 1.0.7 MODEL FITTING Coot 0.9 MODEL REFINEMENT PHENIX 1.19 FINAL EULER ASSIGNMENT cryoSPARC 3.1.0 CLASSIFICATION cryoSPARC 3.0.1 RECONSTRUCTION cryoSPARC 3.1.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION