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Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map)
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 6.701 f_angle_d 0.592 f_chiral_restr 0.041 f_plane_restr 0.006 f_bond_d 0.003
Sample Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide
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 227973 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Composite map of two locally refined maps - resolution of 3.35 and 3.75 respectively. Compositing performed in ChimeraX by vop maximum. Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 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) 64
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 900 Maximum Defocus (nm) 2400 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 105000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC MODEL FITTING UCSF ChimeraX INITIAL EULER ASSIGNMENT cryoSPARC FINAL EULER ASSIGNMENT cryoSPARC CLASSIFICATION cryoSPARC RECONSTRUCTION cryoSPARC MODEL REFINEMENT ISOLDE MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1009886 Blob picking in cryoSPARC Live