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Complex structure of Neuropeptide Y Y2 receptor in complex with NPY and Gi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7DDZ experimental model PDB 7VGX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.321 f_angle_d 0.431 f_chiral_restr 0.039 f_plane_restr 0.003 f_bond_d 0.002
Sample Complex structure of NPY-Y2R-Gi-scFv16 Sample Components Guanine nucleotide-binding protein scFv16 NPY
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 500366 Reported Resolution (Å) 3.11 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7DDZ, 7VGX, 7VGX, 7VGX, 7VGX) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 66
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2250 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 3.2 CTF CORRECTION cryoSPARC 3.2 MODEL FITTING PHENIX 1.19.2-4158 MODEL REFINEMENT PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC 3.2 FINAL EULER ASSIGNMENT cryoSPARC 3.2 RECONSTRUCTION cryoSPARC 3.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 9842630