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Atomic structure and conformational variability of the HER2-Trastuzumab-Pertuzumab complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold experimental model PDB 1N8Z experimental model PDB 1S78 experimental model PDB 6OGE
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.134 f_angle_d 0.702 f_chiral_restr 0.046 f_bond_d 0.007 f_plane_restr 0.006
Sample Ternary complex of her2-trastuzumab-pertuzumab Fabs
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 711008 Reported Resolution (Å) 3.3 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (1n8z, 1s78, 1s78, 6oge) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2600 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.1 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 240000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.3.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.1.2 MODEL FITTING UCSF ChimeraX 1.4 MODEL FITTING PHENIX 1.20.1 MODEL FITTING Coot 0.8.9.2 MODEL REFINEMENT PHENIX 1.20.1 MODEL REFINEMENT Coot 0.8.9.2 INITIAL EULER ASSIGNMENT cryoSPARC 4.1.2 FINAL EULER ASSIGNMENT cryoSPARC 4.1.2 CLASSIFICATION cryoSPARC 4.1.2 RECONSTRUCTION cryoSPARC 4.1.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 2954825