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Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6XKL
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.055 f_angle_d 0.381 f_chiral_restr 0.038 f_plane_restr 0.003 f_bond_d 0.001
Sample Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation in complex with the 6C10 Fab Sample Components Fab fragment of the 6C10 human monoclonal antibody Structure of a SARS-CoV-2 spike S2 subunit in a pre-fusion, open conformation
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 6 seconds blotting time at force 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 408064 Reported Resolution (Å) 2.93 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6xkl) 2 (6xkl) Refinement Space REAL Refinement Protocol OTHER OTHER Refinement Target Cross-correlation coefficient Overall B Value 150 Fitting Procedure Details COOT model building and refinament
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 600 Maximum Defocus (nm) 1800 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 75000 Calibrated Magnification 75757 Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Warp 1.09 IMAGE ACQUISITION EPU 2.12 CTF CORRECTION Warp 1.09 INITIAL EULER ASSIGNMENT cryoSPARC 4.0 FINAL EULER ASSIGNMENT cryoSPARC 4.0 CLASSIFICATION cryoSPARC 4.0 RECONSTRUCTION cryoSPARC 4.0 MODEL REFINEMENT PHENIX 1.20.1_4487:1.21 MODEL REFINEMENT Coot 0.9.5
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 407314