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SARS-COV-2 BA.1 Spike incomplex with VacBB-665
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7T9L
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.286 f_angle_d 0.544 f_chiral_restr 0.043 f_plane_restr 0.005 f_bond_d 0.002
Sample Complex of SARS-COV-2 BA.1 Spike RBD and VacBB-665 Sample Components SARS-COV-2 BA.1 Spike RBD VacBB-665
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot for 5s, waiting for 2.5s, blot force 0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 164748 Reported Resolution (Å) 3.99 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7T9L) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 QUANTUM (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 2500 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf 1.18 MODEL FITTING UCSF Chimera 1.16 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX 1.20
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4699769