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Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A1JQ97-F1
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 4.258 f_angle_d 0.516 f_chiral_restr 0.042 f_bond_d 0.004 f_plane_restr 0.003
Sample Cryo-EM Structure of the 11-Mer ATPase Complex YsaN from the Type III Secretion System of Yersinia enterocolitica
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 174701 Reported Resolution (Å) 3.51 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON IV (4k x 4k) FEI FALCON IV (4k x 4k) Electron Dose (electrons/Å**2) 40 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS TALOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 150000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.6.2 IMAGE ACQUISITION EPU CTF CORRECTION cryoSPARC 4.6.2 MODEL FITTING UCSF ChimeraX 1.9 MODEL FITTING Coot 0.9.8.95 INITIAL EULER ASSIGNMENT cryoSPARC 4.6.2 FINAL EULER ASSIGNMENT cryoSPARC 4.6.2 CLASSIFICATION cryoSPARC 4.6.2 RECONSTRUCTION cryoSPARC 4.6.2 MODEL REFINEMENT PHENIX 1.21.2_5419:
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION