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Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MG8
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.4885 f_angle_d 0.6979 f_chiral_restr 0.0417 f_plane_restr 0.0039 f_bond_d 0.0037
Sample Complex between Hedgehog receptor PTCH1 and nanobody TI23 Sample Components Hedgehog receptor Patched PTCH1 nanobody TI23
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 307652 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6MG8) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 85.6
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) Maximum Defocus (nm) 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 SerialEM CTF CORRECTION CTFFIND 4 MODEL FITTING PHENIX MODEL REFINEMENT PHENIX INITIAL EULER ASSIGNMENT cryoSPARC 2 FINAL EULER ASSIGNMENT cryoSPARC 2 CLASSIFICATION cryoSPARC 2 RECONSTRUCTION cisTEM 1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 3621265 Particles were picked first using a Gaussian blob as the template and then were re-picked using the 2D classes generated from the first round.