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SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7 (focused refinement on Fab-RBD interface)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XKL experimental model PDB 6N16
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.357 f_angle_d 0.634 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Sample SARS-CoV-2 spike glycoprotein trimer complexed with Fab fragment of anti-RBD antibody E7
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 198525 Reported Resolution (Å) 4.03 Resolution Method FSC 0.143 CUT-OFF Other Details Local refinement in cryoSPARC Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6XKL, 6N16, 6N16) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 31.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2400 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 IMAGE ACQUISITION SerialEM 3.8.6 CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING UCSF Chimera 1.16 MODEL FITTING Coot 0.8.9.2-pre MODEL REFINEMENT Coot 0.8.9.2-pre MODEL REFINEMENT PHENIX 1.20.1-4487 INITIAL EULER ASSIGNMENT RELION 4.0-beta-2-commit-543db0 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1+220215 RECONSTRUCTION cryoSPARC 3.3.1+220215
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 402809