8EKC

Escherichia coli 70S ribosome bound to thermorubin, deacylated P-site tRNAfMet and aminoacylated A-site Phe-tRNA


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K00 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.954
f_angle_d0.719
f_chiral_restr0.045
f_bond_d0.007
f_plane_restr0.006
Sample
Escherichia coli 70S ribosome bound to thermorubin, deacylated P-site tRNAfMet and aminoacylated A-site Phe-tRNA
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentLEICA EM GP
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles310702
Reported Resolution (Å)2.7
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (7K00)
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2300
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification96000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC3.3.2
IMAGE ACQUISITIONEPU2.11.1
CTF CORRECTIONcryoSPARC3.3.2
MODEL FITTINGUCSF Chimera1.14
MODEL FITTINGCoot0.8.9.1
INITIAL EULER ASSIGNMENTcryoSPARC3.3.2
FINAL EULER ASSIGNMENTcryoSPARC3.3.2
CLASSIFICATIONcryoSPARC3.3.2
RECONSTRUCTIONcryoSPARC3.3.2
MODEL REFINEMENTPHENIX1.19.2
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION982190