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Cryo-EM structure for a 3:3 complex between mouse leptin and the mouse LEP-R ectodomain (local refinement)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Z3R
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.2816 f_angle_d 1.095 f_chiral_restr 0.0638 f_plane_restr 0.0061 f_bond_d 0.0048
Sample Stucture of mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 54708 Reported Resolution (Å) 4.42 Resolution Method FSC 0.143 CUT-OFF Other Details The final map was obtained via local refinement in cryoSPARC using a mask around the mouse leptin:LEP-R core region of the trimeric complex Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7Z3R) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 45
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 1200 Maximum Defocus (nm) 2500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode OTHER Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC v3.3.1 CTF CORRECTION cryoSPARC v3.3.1 MODEL FITTING UCSF Chimera MODEL REFINEMENT PHENIX 1.19.2-4158 INITIAL EULER ASSIGNMENT cryoSPARC v3.3.1 FINAL EULER ASSIGNMENT cryoSPARC v3.3.1 CLASSIFICATION cryoSPARC v3.3.1 RECONSTRUCTION cryoSPARC v3.3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 141157