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Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LPN
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.253 f_angle_d 0.787 f_chiral_restr 0.077 f_plane_restr 0.008 f_bond_d 0.005
Sample Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 199205 Reported Resolution (Å) 3.52 Resolution Method FSC 0.5 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7LPN) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 82.9 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 58.06
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN 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 FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 103000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3 IMAGE ACQUISITION Leginon CTF CORRECTION cryoSPARC 3 MODEL FITTING Coot MODEL REFINEMENT PHENIX CLASSIFICATION cryoSPARC 3 RECONSTRUCTION cryoSPARC 3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 566072 Blob pick in cryoSparc