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SARS-CoV-2 BA.2 spike RBD in complex bound with VacBB-551
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XB0
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.663 f_angle_d 0.478 f_chiral_restr 0.043 f_bond_d 0.003 f_plane_restr 0.003
Sample Complex of SARS-COV-2 spike RBD and VacBB-551 Sample Components SARS-COV-2 spike RBD VacBB-551
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot for 5s, wait for 2s, blot force:0
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 506671 Reported Resolution (Å) 2.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7XB0) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value 53.8 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (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) 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.2 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.18 MODEL FITTING UCSF Chimera 1.16 MODEL REFINEMENT PHENIX 1.20 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 CLASSIFICATION cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 5391498