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Structure of the mycobacterial ESX-5 Type VII Secretion System hexameric pore complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B9F
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.8701 f_angle_d 1.0254 f_chiral_restr 0.0607 f_plane_restr 0.0078 f_bond_d 0.0064
Sample Hexameric ESX-5 complex from Mycobacterium xenopi: EccB5, EccC5, EccD5-1, EccD5-2, EccE
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 121974 Reported Resolution (Å) 3.4 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7B9F) Refinement Space REAL Refinement Protocol OTHER Refinement Target Overall B Value Fitting Procedure Details Model was initially fitted using ChimeraX and then completed manually using Coot and ISOLDE.
Data Acquisition Detector Type GATAN K3 BIOQUANTUM (6k x 4k) Electron Dose (electrons/Å**2) 49.34
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 700 Maximum Defocus (nm) 1700 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 130000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 2.14 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 2.14 MODEL FITTING Coot 0.9-pre MODEL FITTING ISOLDE 1.1.0 MODEL FITTING UCSF Chimera 1.14 INITIAL EULER ASSIGNMENT cryoSPARC 2.14 FINAL EULER ASSIGNMENT cryoSPARC 2.14 RECONSTRUCTION cryoSPARC 2.14 MODEL REFINEMENT PHENIX 1.18.2
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION