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PKD2 ion channel, F629S variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.065 f_angle_d 0.41 f_chiral_restr 0.036 f_plane_restr 0.003 f_bond_d 0.002
Sample PKD2 ion channel F629S variant protomer
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Vitrification carried in air. Ethane temperature -183 C
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 215875 Reported Resolution (Å) 2.76 Resolution Method FSC 0.143 CUT-OFF Other Details Final reconstruction performed with C4 symmetry imposed Refinement Type Symmetry Type POINT Point Symmetry C4
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol Refinement Target Overall B Value 107.9 Fitting Procedure Details The initial Alphafold model was fitted to the map using ChimeraX. Refinement was performed using ISOLDE and PHENIX.
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 60
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 600 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 PARTICLE SELECTION cryoSPARC 4.5 IMAGE ACQUISITION SerialEM v4.1.0beta CTF CORRECTION cryoSPARC 4.5 MODEL FITTING UCSF ChimeraX 1.8 MODEL FITTING ISOLDE 1.8 INITIAL EULER ASSIGNMENT cryoSPARC 4.5 FINAL EULER ASSIGNMENT cryoSPARC 4.5 CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC 4.5 MODEL REFINEMENT ISOLDE 1.8 MODEL REFINEMENT PHENIX 1.21.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1046126 Denoised micrographs were blob picked (130-170 angstrom)