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Cryo-EM structure of human VPS34-CI with ADP:MgF3
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 6.817 f_angle_d 0.591 f_chiral_restr 0.044 f_plane_restr 0.005 f_bond_d 0.003
Sample Protein complex VPS34-CI with NRBF2 MIT and ADP:MgF3 Sample Components Human VPS34-CI NRBF2 MIT domain
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK II Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.5 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Number of Particles 186859 Reported Resolution (Å) 3.66 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (9TW2) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k 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) 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 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION crYOLO 1.7.5 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING UCSF ChimeraX 1.7.1 MODEL FITTING ISOLDE 1.7.1 MODEL REFINEMENT TEMPy 1.2.0 MODEL REFINEMENT PHENIX 1.21.2_5419 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2 PARTICLE SELECTION crYOLO 1.7.5 CTF CORRECTION cryoSPARC 4.6.2 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 306134 PHASE FLIPPING AND AMPLITUDE CORRECTION 306134