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Structure of the SARS-CoV-2 S S1 doamin in complex with the mouse antibody Fab fragment, HSW-2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SC1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.648 f_angle_d 0.508 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Sample SARS-CoV-2 S 6P in complex with HSW-2 Fab Sample Components Severe acute respiratory syndrome coronavirus 2 spike glycoprotein S1 domain HSW-2 Fab VH and VL domains HSW-2 Fab CH1 and CL domains
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 43362 Reported Resolution (Å) 4.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7SC1) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value 87 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 TALOS ARCTICA 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 45000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 3.2 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2 MODEL REFINEMENT PHENIX 1.19.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 449736