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Cryo-EM structure of CH235.12 in complex with HIV-1 Env trimer CH505TF.N279K.SOSIP.664 with high-mannose glycans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UDA experimental model PDB 5F96
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.851 f_angle_d 0.809 f_chiral_restr 0.051 f_plane_restr 0.005 f_bond_d 0.004
Sample Trimeric HIV-1 Env in complex with CH235.12
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument Cryogen Name ETHANE Sample Vitrification Details BLOT FOR 2.5 S BEFORE PLUNGING
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 53398 Reported Resolution (Å) 4.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6UDA, 5F96) Refinement Space Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 66.71
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 750 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION Latitude CTF CORRECTION cryoSPARC MODEL FITTING UCSF Chimera MODEL FITTING Coot MODEL FITTING RosettaEM MODEL REFINEMENT Coot MODEL REFINEMENT PHENIX MODEL REFINEMENT ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION