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Full-length P-Rex1 in complex with inositol 1,3,4,5-tetrakisphosphate (IP4)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PCV experimental model PDB 6VSK experimental model PDB 5D3X experimental model PDB 5FI1 experimental model PDB 7RX9
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9598 f_angle_d 0.5584 f_chiral_restr 0.0365 f_bond_d 0.0042 f_plane_restr 0.0039
Sample Complex of full-length Phosphatidylinositol 3,4,5-trisphosphate (PIP3)-dependent Rac exchanger 1 (P-Rex1) bound to inositol 1,3,4,5-tetrakisphosphate (IP4)
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 187734 Reported Resolution (Å) 4.1 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6PCV, 6VSK, 5D3X, 5FI1, 7RX9) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 57.8
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 200 Maximum Defocus (nm) 2000 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 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version 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 2426612 806,067 particles untilted and 1,620,545 particles tilted