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Designed antibody vAB66 targeting PAP-HLA A*02:01
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7YV1 experimental model PDB 3SOB experimental model PDB 7SRO experimental model PDB 9NMV
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.0187 f_angle_d 0.5274 f_chiral_restr 0.0426 f_plane_restr 0.0047 f_bond_d 0.0025
Sample vAB-66 Fab bound to HLA-A*02:01 displaying PAP peptide with AD01 nanobofy fiducial Sample Components HLA A*02:01 displaying PAP peptide vAB66 Fab HLA A*02:01 PAP peptide AD01 nanobody
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 880830 Reported Resolution (Å) 2.5 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7YV1, 3SOB, 7SRO, 9NMV) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2 MODEL REFINEMENT PHENIX 1.21.2_5419
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION patch correction 6762787 template picks based on 2D-classified blob picks