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CryoEM structure of human polycystin-2/PKD2 in UDM supplemented with PI(4,5)P2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5K47
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.006 f_angle_d 1.005 f_chiral_restr 0.056 f_bond_d 0.011 f_plane_restr 0.006
Sample POLYCYSTIN-2 CHANNEL TETRAMER
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 51694 Reported Resolution (Å) 2.96 Resolution Method FSC 0.143 CUT-OFF Other Details RELION autorefinement. Unmasked resolution is 3.12. After masking to remove the detergent micelle resolution is 2.96A Refinement Type Symmetry Type POINT Point Symmetry C4
Map-Model Fitting and Refinement Id 1 (5K47) Refinement Space REAL Refinement Protocol AB INITIO MODEL Refinement Target Overall B Value 85 Fitting Procedure Details
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 52.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1000 Maximum Defocus (nm) 2500 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 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Gautomatch 0.53 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND v.4.1.10 MODEL FITTING Coot MODEL REFINEMENT PHENIX 1.13 INITIAL EULER ASSIGNMENT RELION 3 FINAL EULER ASSIGNMENT RELION 3 CLASSIFICATION RELION 3 RECONSTRUCTION RELION 3
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 98113