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Complex structure of HIV superinfection Fab QA013.2 and BG505.SOSIP.664
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ACO
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.493 f_angle_d 1.123 f_chiral_restr 0.064 f_bond_d 0.011 f_plane_restr 0.007
Sample Complex of HIV-1 envelope protein with super-infection Fab QA013.2
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3ul sample volume, blotted for 3-4 seconds
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 113470 Reported Resolution (Å) 4.15 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
Map-Model Fitting and Refinement Id 1 (5ACO) Refinement Space Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Rigid body fitting in Chimera, followed by real space refinement in Phenix using reference model restraints
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 44
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1700 Maximum Defocus (nm) 3500 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 110000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details Preliminary grid screening was performed manually
EM Software Task Software Package Version CTF CORRECTION CTFFIND 4.1 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION RECONSTRUCTION RELION MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1082742 LOG picker