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Type 3 secretion system export apparatus core, inner rod and needle of Shigella flexneri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RWY experimental model PDB 6RWK experimental model PDB 6RWX
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.271 f_angle_d 0.434 f_chiral_restr 0.036 f_plane_restr 0.004 f_bond_d 0.002
Sample Needle complex of the type 3 secretion system Sample Components Export apparatus core Inner rod Needle filament Ring formed by the N1 domain of the secretin MxiD MxiJ loop interacting with the export apparatus
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 90547 Reported Resolution (Å) 4.05 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (6RWY, 6RWK, 6RWX) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value 59.2 Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 25
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 1500 Maximum Defocus (nm) 4000 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 101179 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4.1.13 MODEL FITTING UCSF Chimera 1.15 INITIAL EULER ASSIGNMENT RELION 3.0 FINAL EULER ASSIGNMENT RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT PHENIX 1.18.2_3874
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION