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Asymmetric vertex of the clathrin minicoat cage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SCT
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 6.8189 f_angle_d 0.3393 f_chiral_restr 0.0328 f_plane_restr 0.0028 f_bond_d 0.0012
Sample Natively assembled clathrin coated vesicles
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 305413 Reported Resolution (Å) 6.3 Resolution Method FSC 0.143 CUT-OFF Other Details After the final refinement in cisTEM, half-maps were generated in cisTEM and the FSC was calculated with EMAN FSC tools. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (6SCT, 6SCT, 6SCT) 2 (6SCT, 6SCT, 6SCT) 3 (6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT, 6SCT) Refinement Space Refinement Protocol AB INITIO MODEL AB INITIO MODEL FLEXIBLE FIT 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 FEI TITAN KRIOS Minimum Defocus (nm) 3000 Maximum Defocus (nm) 5000 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 35000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION RELION 3 IMAGE ACQUISITION Leginon CTF CORRECTION cisTEM 1 CTF CORRECTION CTFFIND 4 CTF CORRECTION RELION 3 MODEL FITTING Rosetta INITIAL EULER ASSIGNMENT cryoSPARC 2 FINAL EULER ASSIGNMENT cisTEM 1 FINAL EULER ASSIGNMENT RELION 3 RECONSTRUCTION cisTEM 1 MODEL REFINEMENT PHENIX MODEL FITTING Rosetta MODEL REFINEMENT PHENIX MODEL FITTING Rosetta MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 360000 These are subparticle images that were extracted from particle images. Each minicoat particle has 24 asymmetric vertices. From a total of 15000 minicoat particles, 360000 vertex subparticles were extracted. The position of subparticles was calculated by the localized reconstruction script in scipion, and the subparticle images were extracted with RELION extraction tools.