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Structure of the Salmonella PrgI needle filament attached to the basal body
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2LPZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.982 f_angle_d 0.623 f_chiral_restr 0.045 f_bond_d 0.006 f_plane_restr 0.004
Sample Needle filament of the type III secretion system
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE-PROPANE Sample Vitrification Details
3D Reconstruction Reconstruction Method HELICAL Number of Particles 34174 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type HELICAL Axial Symmetry C1 Axial Rise 4.2 Angular Rotation 64.3
Map-Model Fitting and Refinement Id 1 (2LPZ) Refinement Space REAL Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details Initial automatic modeling with StarMap, a Rosetta plug-in of ChimeraX.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 31
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TITAN KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 3500 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 IMAGE ACQUISITION EPU CTF CORRECTION CTFFIND 4 MODEL FITTING UCSF Chimera 1.14 CLASSIFICATION RELION 3.0 RECONSTRUCTION RELION 3.0 MODEL REFINEMENT Coot 0.8.9.2 MODEL REFINEMENT PHENIX 1.17-3644
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 308303