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Cryo-EM structure of the PI4KA complex bound to an EFR3 interfering nanobody (F3IN)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BAX in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.014 f_angle_d 0.479 f_chiral_restr 0.036 f_plane_restr 0.003 f_bond_d 0.002
Sample Dimer of heterotetramers of PI4KA,TTC7B,FAM126A, and EFR3 interfering nanobody (F3IN) Sample Components PI4KA,TTC7B,FAM126A complex EFR3 interfering nanobody (F3IN)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Blot force -5, blot time 1.5 s.
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 282982 Reported Resolution (Å) 3.54 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C2
Map-Model Fitting and Refinement Id 1 (9BAX) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON III (4k x 4k) Electron Dose (electrons/Å**2) 50
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 165000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version CTF CORRECTION cryoSPARC 4.5.2 MODEL FITTING UCSF ChimeraX 1.8 INITIAL EULER ASSIGNMENT cryoSPARC 4.5.2 FINAL EULER ASSIGNMENT cryoSPARC 4.5.2 CLASSIFICATION cryoSPARC 4.5.2 RECONSTRUCTION cryoSPARC 4.5.2 MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION