7NBU
Structure of the HigB1 toxin mutant K95A from Mycobacterium tuberculosis (Rv1955) and its target, the cspA mRNA, on the E. coli Ribosome.
ELECTRON MICROSCOPY
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 |