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In situ cryo-EM structure of axonal microtubules from ghost neurons (compact lattice)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9NPD
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.286 f_angle_d 0.736 f_chiral_restr 0.047 f_bond_d 0.006 f_plane_restr 0.005
Sample Microtubule, axonal
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details blot force 4, blot time 4 s
3D Reconstruction Reconstruction Method HELICAL Number of Particles 30423 Reported Resolution (Å) 3.96 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 83.11 Angular Rotation
Map-Model Fitting and Refinement Id 1 (9PND) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details iterative rounds of manual building and automated real-space refinement
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 52.2
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 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 4.7 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.7 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8.93 INITIAL EULER ASSIGNMENT cryoSPARC 4.7 FINAL EULER ASSIGNMENT FREALIGN 9.11 CLASSIFICATION cryoSPARC 4.7 RECONSTRUCTION cryoSPARC 4.7 MODEL REFINEMENT PHENIX 2.0-5936
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 158108