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Modified BG505 SOSIP-based immunogen RC1 in complex with the elicited V3-glycan patch bNAb 10-1074
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5T3Z
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.299 f_angle_d 0.833 f_chiral_restr 0.114 f_bond_d 0.007 f_plane_restr 0.005
Sample Complex of RC1 variant of BG505 SOSIP.664 trimer with three 10-1074 Fabs and three CD4bs Fabs Sample Components RC1 variant of BG505 SOSIP.664 trimer 10-1074 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 0 blot force, 3.5 second blot time, 3 uL sample added to freshly glow-discharged grids
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 122013 Reported Resolution (Å) 4.05 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (5T3Z, 5T3Z, 5T3Z, 5T3Z) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 1000 Maximum Defocus (nm) 3400 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 73000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3 IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.14 INITIAL EULER ASSIGNMENT cryoSPARC 2.1 FINAL EULER ASSIGNMENT cryoSPARC 2.1 CLASSIFICATION cryoSPARC 2.1 RECONSTRUCTION cryoSPARC 2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION