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The CryoEM structure of N49-P9.6-FR3 and PGT121 Fabs in complex with BG505 SOSIP.664
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CDI experimental model PDB 5CEZ experimental model PDB 7SX7
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.36 f_angle_d 0.687 f_chiral_restr 0.054 f_plane_restr 0.005 f_bond_d 0.004
Sample One BG505 SOSIP.644 trimer in complex with three N49-P9.6-FR3 Fabs and three PGT121 Fabs.
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 132055 Reported Resolution (Å) 4.02 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, 6CDI, 6CDI, 6CDI, 6CDI, 6CDI, 5CEZ, 5CEZ, 5CEZ, 5CEZ, 5CEZ, 5CEZ, 7SX7, 7SX7, 7SX7, 7SX7, 7SX7, 7SX7) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 58.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2700 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode OTHER Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM IMAGE ACQUISITION cryoSPARC CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT UCSF ChimeraX FINAL EULER ASSIGNMENT PHENIX CLASSIFICATION cryoSPARC RECONSTRUCTION PHENIX MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY 3151423