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PDCoV S RBD bound to PD41 Fab (local refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BFU in silico model Other
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.67 f_angle_d 0.6925 f_chiral_restr 0.0489 f_bond_d 0.0065 f_plane_restr 0.0057
Sample PDCoV S RBD complex with PD41 Fab (local refinement)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blotting time 6 seconds, force -1
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 438204 Reported Resolution (Å) 2.8 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6bfu) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 1800 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION RELION 5 CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.21.1_5286 MODEL REFINEMENT ISOLDE
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5732849