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core filament of the spirochete periplasmic flagella of Leptospira biflexa from the deleted fcpB_CL13 strain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LRZ
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.794 f_angle_d 0.493 f_chiral_restr 0.035 f_bond_d 0.003 f_plane_restr 0.003
Sample core filament of the spirochete periplasmic flagella from the deleted fcpB_CL13 strain
Specimen Preparation Sample Aggregation State FILAMENT Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 1436926 Reported Resolution (Å) 3.2 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (9LRZ) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 40
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 500 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 0.01 Imaging Mode BRIGHT FIELD Specimen Holder Model FEI TITAN KRIOS AUTOGRID HOLDER Nominal Magnification 81000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 4.2.1 IMAGE ACQUISITION SerialEM CTF CORRECTION cryoSPARC 4.2.1 MODEL FITTING Coot 0.9.8.7 MODEL REFINEMENT PHENIX 1.21.1_5286 INITIAL EULER ASSIGNMENT cryoSPARC 4.2.1 FINAL EULER ASSIGNMENT cryoSPARC 4.2.1 CLASSIFICATION cryoSPARC 4.2.1 RECONSTRUCTION cryoSPARC 4.2.1
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING ONLY