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Structure of human NHE6.1 bound to PIP2
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 12.6677 f_angle_d 0.5603 f_chiral_restr 0.0373 f_plane_restr 0.0047 f_bond_d 0.0028
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 586700 Reported Resolution (Å) 2.55 Resolution Method FSC 0.143 CUT-OFF Other Details 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 INITIAL EULER ASSIGNMENT cryoSPARC 3.3.1 FINAL EULER ASSIGNMENT cryoSPARC 3.3.1 CLASSIFICATION cryoSPARC 3.3.1 MODEL REFINEMENT PHENIX 1.21.1_5286
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