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Structure of E. coli LetB delta (Ring6) mutant, Ring 1 in the open state (Model 2, Rings 1-3 only)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V0D
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.005 f_angle_d 0.653 f_chiral_restr 0.043 f_bond_d 0.005 f_plane_restr 0.003
Sample Homohexameric complex of delta (Ring6) mutant form of LetB
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details 3 second blot time and blot force of 5 before plunge freezing
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 39547 Reported Resolution (Å) 3.55 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C6
Map-Model Fitting and Refinement Id 1 (6V0D) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type GATAN K3 (6k x 4k) Electron Dose (electrons/Å**2) 56.3
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS KRIOS Minimum Defocus (nm) 800 Maximum Defocus (nm) 2200 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 37000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC 2.1 IMAGE ACQUISITION SerialEM CTF CORRECTION CTFFIND 4.1 MODEL FITTING Coot 0.9 MODEL REFINEMENT PHENIX 1.18.2 INITIAL EULER ASSIGNMENT cryoSPARC 2.1 FINAL EULER ASSIGNMENT RELION 3.1.0 CLASSIFICATION RELION 3.1.0 RECONSTRUCTION RELION 3.1.0
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 739130 Template picking followed by iterative rounds of 2D classification