9CAI

High-resolution C. elegans 80S ribosome structure - class 1


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.6553
f_angle_d0.5564
f_chiral_restr0.0405
f_plane_restr0.0045
f_bond_d0.0035
Sample
Caenorhabditis elegans 80S ribosome
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles145659
Reported Resolution (Å)2.59
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value59.4
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K3 BIOCONTINUUM (6k x 4k)
Electron Dose (electrons/Å**2)40.94
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)500
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC4.4.1
IMAGE ACQUISITIONSerialEMv4.93
CTF CORRECTIONcryoSPARC4.4.1
MODEL FITTINGCoot
MODEL REFINEMENTPHENIX1.20.1_4487:
INITIAL EULER ASSIGNMENTcryoSPARC4.4.1
FINAL EULER ASSIGNMENTcryoSPARC4.4.1
CLASSIFICATIONcryoSPARC4.4.1
RECONSTRUCTIONcryoSPARC4.4.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION695837