ELECTRON MICROSCOPY

Sample

Escherichia coli paused disome complex

Specimen Preperation
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Sample Vitrification Details Withdrawn samples were spotted directly onto freshly glow-discharged holey carbon grids, blotted for 1-2 s, and flash frozen in liquid ethane using a Vitrobot Mark IV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
Map-Model Fitting and Refinement
ID 1
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. 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/Å2) 45
Imaging Experiment
Date of Experiment ?
Temprature (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 ?
Imaging Experiment
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 ?