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Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7K00
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.7552 f_angle_d 0.662 f_chiral_restr 0.0409 f_bond_d 0.0064 f_plane_restr 0.0044
Sample M. tuberculosis HigB1_K95A mutant toxin and its target, the CspA mRNA, on the E. coli Ribosome. Sample Components 30S Ribosomal subunit 50S Ribosomal subunit 16S rRNA 30S ribosomal proteins 23S and 5S rRNA 50S ribosomal proteins P-site fMet-tRNA(fMet) E-site tRNA cspA mRNA HigB1 toxin
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details blot for 2s before plunging
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 13877 Reported Resolution (Å) 3.11 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT
Map-Model Fitting and Refinement Id 1 (7K00) Refinement Space REAL Refinement Protocol RIGID BODY FIT Refinement Target Overall B Value Fitting Procedure Details Initial local fitting was done chain by chain using Chimera. The model was then refine using coot and phenix.
Data Acquisition Detector Type GATAN K2 SUMMIT (4k x 4k) Electron Dose (electrons/Å**2) 52
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model FEI TALOS ARCTICA Minimum Defocus (nm) 700 Maximum Defocus (nm) 2500 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 120000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION cryoSPARC IMAGE ACQUISITION SerialEM CTF CORRECTION Gctf MODEL FITTING UCSF Chimera 1.13.1 INITIAL EULER ASSIGNMENT RELION 3.1 FINAL EULER ASSIGNMENT RELION 3.1 CLASSIFICATION RELION 3.1 RECONSTRUCTION RELION 3.1 MODEL REFINEMENT PHENIX 1.18.2-3874 MODEL REFINEMENT Coot 0.9 EL (ccp4)
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 294820