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SARS-CoV-2 (wuhan variant) Spike protein in complex with the single chain fragment scFv76-77 (focused refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZCE
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.236 f_angle_d 0.528 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.002
Sample SARS-CoV-2 Spike protein in complex with the single chain fragment scFv76 Sample Components SARS-CoV-2 Spike protein scFv76-77 single chain fragment
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 42716 Reported Resolution (Å) 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 (7zce) Refinement Space Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 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 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.0.9 IMAGE ACQUISITION EPU 2.8 CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details NONE 242907