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Local refinement of SARS-CoV-2 BA.2.86 Spike and XBB-7 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8CIM
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.062 f_angle_d 0.582 f_chiral_restr 0.045 f_plane_restr 0.005 f_bond_d 0.003
Sample BA-2.86 variant SARS-CoV2 S protein complexed with XBB-7 fab. Sample Components XBB-7 fab BA.2.86 variant SARS-CoV2 S protein
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 75021 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Determined by cryoSPARC. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (8CIM) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Phenix real space refinement with manual checks using coot.
Data Acquisition Detector Type FEI FALCON IV (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) 800 Maximum Defocus (nm) 2600 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 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC MODEL FITTING Coot MODEL FITTING PHENIX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Determined using cryoSPARC live patch CTF correction. 524958