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Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, R40-1G8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K8T experimental model PDB 7K8O
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.848 f_angle_d 0.576 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.004
Sample SARS-CoV-2 S 6P in complex with R40-1G8 Sample Components R40-1G8 Fab Severe acute respiratory syndrome coronavirus 2 spike glycoprotein
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 178597 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (7K8T, 7K8O) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 135 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3000 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 3.2 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.2 MODEL FITTING UCSF Chimera 1.13.1 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT PHENIX 1.19
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 840417