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Structure of human NHE6.1 bound to PIP2 (core-TM domain)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Q92581
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.1344 f_angle_d 0.6393 f_chiral_restr 0.0397 f_plane_restr 0.0054 f_bond_d 0.0037
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Sample vol 3ul; blot force -5; Blot time 9s; Wait time 20sec
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 153800 Reported Resolution (Å) 2.33 Resolution Method FSC 0.143 CUT-OFF Other Details cryoSPARC non-uniform refinement of CROSIEVED particles Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details Initial model fitted and manually rebuilt/refined in COOT and final refinement in ISOLDE and PHENIX
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 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 Topaz 0.2.4 PARTICLE SELECTION cryoSPARC 3.3.1 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 3.3.1 MODEL FITTING Coot 0.9.8.93 MODEL FITTING ISOLDE 1.3 MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 RECONSTRUCTION cryoSPARC 3.3.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION Patch CTF in cryoSPARC 1090375 Blob picked particles from a subset of micrographs were used to train a TOPAZ model for picking