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Cryo-EM structure of vaccine-elicited antibody 0PV-a.01 in complex with HIV-1 Env BG505 DS-SOSIP and antibodies VRC03 and PGT122
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CDI
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.954 f_angle_d 1.471 f_chiral_restr 0.081 f_bond_d 0.014 f_plane_restr 0.01
Sample HIV-1 Env BG505 DS-SOSIP and antibodies 0PV-a.01, VRC03 and PGT122 Sample Components Envelope glycoprotein gp120 Envelope glycoprotein gp41 VRC03 PGT122 0PV-a.01
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument SPOTITON Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 55345 Reported Resolution (Å) 4.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (6CDI) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 70.49
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION DoG Picker IMAGE ACQUISITION Leginon CTF CORRECTION CTFFIND 4 MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC 2 RECONSTRUCTION cryoSPARC 2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION