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Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with broadly neutralizing llama nanobody R27 targeting the CD4-binding site
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 6.528 f_angle_d 0.677 f_chiral_restr 0.052 f_plane_restr 0.004 f_bond_d 0.003
Sample Complex between HIV-1 Env BG505 DS-SOSIP and llama nanobody R27
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 315969 Reported Resolution (Å) 3.58 Resolution Method FSC 0.5 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C3
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 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) 1000 Maximum Defocus (nm) 2500 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 22500 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3 IMAGE ACQUISITION SerialEM 4.09 CTF CORRECTION cryoSPARC 3 MODEL FITTING Coot RECONSTRUCTION cryoSPARC 3 MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2549097 Blob pick in cryoSparc