8BHN

Elongating E. coli 70S ribosome containing deacylated tRNA(iMet) in the P-site and m6AAA mRNA codon with cognate dipeptidyl-tRNA(Lys) in the A-site


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.74
f_angle_d0.534
f_chiral_restr0.036
f_plane_restr0.004
f_bond_d0.003
Sample
Elongating E. coli 70S ribosome with deacylated tRNA(iMet) in the P-site and mRNA containing m6AAA codon and dipeptidyl-tRNA(Lys) in the A-site
Sample Components
50S subunit
30S subunit
23S and 5S rRNA
16S rRNA
mRNA and tRNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles41219
Reported Resolution (Å)2.85
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id12
Refinement SpaceREALREAL
Refinement ProtocolRIGID BODY FITFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsFollowing rigid body fitting we used online Namdiantor tool to perform initial flexible fitting: https://namdinator.au.dk/namdinator/
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)900
Maximum Defocus (nm)2100
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification105000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.0
IMAGE ACQUISITIONEPU2.1
CTF CORRECTIONcryoSPARC3.3.0
MODEL FITTINGUCSF ChimeraX1.2.5
MODEL REFINEMENTPHENIXOnline
MODEL FITTINGISOLDE1.4
MODEL REFINEMENTPHENIX1.19.2-4158
INITIAL EULER ASSIGNMENTcryoSPARC3.3.0
CLASSIFICATIONcryoSPARC3.3.0
RECONSTRUCTIONcryoSPARC3.3.0
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION500