9B1Y | pdb_00009b1y

WT strain WT mycobacterial ribosome

ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5O60
experimental model	PDB	5O5J

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	17.6431
f_angle_d	0.6618
f_chiral_restr	0.0374
f_plane_restr	0.0076
f_bond_d	0.0059

Sample
Mycobacterium smegmatis ribosome, WT strain WT

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	1466881
Reported Resolution (Å)	2.47
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (5o60, 5o5j)
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)	901.165

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	400
Maximum Defocus (nm)	1400
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	96000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cisTEM	development
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cisTEM	development
MODEL FITTING	UCSF ChimeraX
MODEL FITTING	ISOLDE
MODEL FITTING	Coot
MODEL FITTING	PyMOL
INITIAL EULER ASSIGNMENT	cisTEM	development
FINAL EULER ASSIGNMENT	cisTEM	development
CLASSIFICATION	cisTEM	development
RECONSTRUCTION	cisTEM	development
MODEL REFINEMENT	PHENIX	1.20_4459
MODEL REFINEMENT	ISOLDE

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.