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PKD2 ion channel, F634A mutant
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 4.611 f_angle_d 0.445 f_chiral_restr 0.037 f_bond_d 0.004 f_plane_restr 0.003
Sample PKD2 ion channel F634A mutant 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 98122 Reported Resolution (Å) 3.01 Resolution Method FSC 0.143 CUT-OFF Other Details Final reconstruction was generated using C4 symmetry 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 101 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 1441572 Micrographs were blob picked (130-170 angstrom)