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B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CH9
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 9.0013 f_angle_d 1.2127 f_chiral_restr 0.0729 f_bond_d 0.0082 f_plane_restr 0.0077
Sample Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab Sample Components B41 SOSIP.664 trimer 10-1074 Fab SF12 Fab
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 301920 Reported Resolution (Å) 3.28 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6CH9, 6CH9) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 3000 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION Gctf 1.06 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC 2.1 FINAL EULER ASSIGNMENT RELION 3.0 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX 1.14
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 676161 manual picking followed by template-based autopicking