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HER2/ErbB2 extracellular domain (ECD) in extended conformation in complex with trastuzumab (TZB) antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MY6
Sample Ternary complex of HER2/ErbB2 in its canonical conformation with trastuzumab (TZB) antibody.
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 77784 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5MY6) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Cross-correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 72.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2400 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 MODEL FITTING UCSF Chimera INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC 4.4 CLASSIFICATION cryoSPARC CLASSIFICATION Xmipp MODEL REFINEMENT Coot 0.9.6 MODEL REFINEMENT PHENIX 1.21.1_5286: MODEL REFINEMENT RosettaEM 2024.09+release.06b3cf8ad0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 4207722