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Structure of the TSC:WIPI3 lysosomal recruitment complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold P49815 in silico model AlphaFold Q92574 experimental model PDB 5EJC experimental model PDB 9C9I
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.738 f_angle_d 0.664 f_chiral_restr 0.044 f_plane_restr 0.006 f_bond_d 0.005
Sample TSC:WIPI3 lysosomal recruitment complex (composite map)
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 200000 Reported Resolution (Å) 2.9 Resolution Method FSC 0.143 CUT-OFF Other Details The global resolution of this composite is estimated based on the voxel average of focused reconstructions. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5EJC, 9C9I) Refinement Space REAL Refinement Protocol OTHER Refinement Target Cross-correlation coefficient Overall B Value 96.4 Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 46.54
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 3000 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 cryoSPARC 4.0.1 PARTICLE SELECTION Topaz PARTICLE SELECTION crYOLO IMAGE ACQUISITION EPU 2.12.1.2782 CTF CORRECTION CTFFIND MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT cryoSPARC 4.0.1 FINAL EULER ASSIGNMENT cryoSPARC 4.0.1 FINAL EULER ASSIGNMENT RELION 4.0 CLASSIFICATION RELION 4.0 MODEL REFINEMENT PHENIX MODEL REFINEMENT Coot MODEL REFINEMENT ISOLDE
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 1176292 Template picking, blob picking, TOPAZ, crYOLO