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Structure of the SARS-CoV-2 BA.1 spike with UT28-RD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DZH experimental model PDB 7X7O
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.0843 f_angle_d 0.9319 f_chiral_restr 0.0599 f_bond_d 0.0119 f_plane_restr 0.0063
Sample SARS-CoV-2 BA.1 spike protein with UT28K-RD complex Sample Components SARS-CoV-2 BA.1 spike protein UT28K-RD Fab
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 179684 Reported Resolution (Å) 3.22 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8DZH, 7X7O) 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) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1300 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 3.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.20.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1146148