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Cryo-EM map of SARS-CoV-2 Omicron BA.2 spike in complex with 2130-1-0114-112
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7L7E
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.646 f_angle_d 0.691 f_chiral_restr 0.044 f_plane_restr 0.008 f_bond_d 0.004
Sample SARS Cov2 Omicron BA.2 RBD complex with Fab LLNL-199 Sample Components SARS Cov2 Omicron BA.2 RBD Fab LLNL-199
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 386950 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7L7E, 7L7E, 7L7E) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 52.173
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION 4 FINAL EULER ASSIGNMENT RELION 4 CLASSIFICATION RELION 4 RECONSTRUCTION RELION 4 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION