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Structure of SARS-CoV-2 spike RBD in complex with neutralizing antibody NIV-11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6M0J
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.27 f_angle_d 0.559 f_chiral_restr 0.043 f_plane_restr 0.004 f_bond_d 0.003
Sample SARS-COV-2 spike glycoprotein in complex with NIV-11 Sample Components SARS-CoV-2 spike glycoprotein NIV-11 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blotting time 5 s and blotting force 5.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 80132 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6M0J) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 51.41
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2300 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF Chimera 1.15 MODEL REFINEMENT PHENIX 1.20 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION RELION 3.1.3 RECONSTRUCTION cryoSPARC 3.3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1498301