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Cryo-EM structure of SARS-CoV-2 spike (HexaPro variant) in complex with nanobody W25 (map 3, focus refinement on RBD, W25 and adjacent NTD)
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.897 f_angle_d 0.638 f_chiral_restr 0.048 f_plane_restr 0.006 f_bond_d 0.003
Sample Severe acute respiratory syndrome coronavirus 2 spike protein in complex with nanobody W25
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 1s blotting time
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 132634 Reported Resolution (Å) 5.92 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI POLARA 300 Minimum Defocus (nm) 500 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode OTHER Specimen Holder Model Nominal Magnification 31000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3.0.7 IMAGE ACQUISITION Leginon CTF CORRECTION CTFFIND 4 MODEL FITTING PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT RELION 3.0.7 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 527691