8SYL

Cryo-EM structure of the Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8EKC 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.27
f_angle_d0.551
f_chiral_restr0.035
f_bond_d0.004
f_plane_restr0.004
Sample
Escherichia coli 70S ribosome in complex with amikacin, mRNA, and A-, P-, and E-site tRNAs
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles234339
Reported Resolution (Å)2.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (8EKC)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40.5852
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)700
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.1.2
IMAGE ACQUISITIONSerialEM
MASKINGcryoSPARC4.1.2
CTF CORRECTIONcryoSPARC4.1.2
MODEL FITTINGUCSF Chimera1.14
MODEL REFINEMENTPHENIX1.19.2.4158
INITIAL EULER ASSIGNMENTcryoSPARC4.1.2
FINAL EULER ASSIGNMENTcryoSPARC4.1.2
CLASSIFICATIONcryoSPARC4.1.2
RECONSTRUCTIONcryoSPARC4.1.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION