8R3V

Escherichia coli paused disome complex (non-rotated disome interface)

ELECTRON MICROSCOPY

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.474
f_angle_d	0.516
f_chiral_restr	0.031
f_plane_restr	0.007
f_bond_d	0.002

Sample
Escherichia coli paused disome complex

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a ...	Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a Vitrobot Mark IV plunger (ThermoFisher Scientific) after a wait time of 40 s at 4 degrees Celsius.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	63618
Reported Resolution (Å)	3.28
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C1

Map-Model Fitting and Refinement
Id	1 (7N1P)
Refinement Space	REAL
Refinement Protocol	OTHER
Refinement Target	CC
Overall B Value	87.2
Fitting Procedure
Details	The atomic model of the E. coli 70S ribosome was initially docked into the postprocessed density maps with UCSF Chimera and manually adjusted in Coot. ...	The atomic model of the E. coli 70S ribosome was initially docked into the postprocessed density maps with UCSF Chimera and manually adjusted in Coot. As the modelled mRNA represents a mixture of all isolated native E. coli mRNAs bound to polysomes, a random sense mRNA sequence was chosen, except for the five codons, which were adjusted to the anticodons. Ligand restraints were generated using phenix.eLBOW. The full-length model for protein bS1 was generated using AlphaFold and manually placed and adjusted in Coot. All models were refined over multiple rounds using the module phenix.real_space_refine in PHENIX and interactive model building and refinement in Coot, using libG restraints for the RNAs. The quality of all refined models was assessed using the comprehensive model validation function in PHENIX and wwPDB validation server.

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	45

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2000
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	81000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	Gautomatch
IMAGE ACQUISITION	EPU	2.8.1
CTF CORRECTION	Gctf
CTF CORRECTION	cryoSPARC	3.3.1
MODEL FITTING	Coot	0.9.6
MODEL FITTING	UCSF Chimera	1.17
INITIAL EULER ASSIGNMENT	cryoSPARC	3.3.1
FINAL EULER ASSIGNMENT	cryoSPARC	3.3.1
CLASSIFICATION	cryoSPARC	3.3.1
RECONSTRUCTION	cryoSPARC	3.3.1
MODEL REFINEMENT	PHENIX	1.20.1_4487
MODEL REFINEMENT	Coot	0.9.6
MODEL REFINEMENT	LIBG	ccp4-8.0

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION		1883839

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 R01GM133198.