9V25 | pdb_00009v25

Cryo- EM structure of large subunit (LSU) of 75S ribosome with A/P- & P/E- tRNAs from Entamoeba histolytica


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherOther 
Sample
Cryo-EM structure of Ribosome large subunit of 75S ribosome with A/P and P/E-tRNA from Entamoeba histolytica
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles39958
Reported Resolution (Å)3
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value48.6
Fitting Procedure
Detailsphenix.real_space_refinement
Data Acquisition
Detector TypeFEI FALCON III (4k x 4k)
Electron Dose (electrons/Å**2)1.106
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)1800
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
Calibrated Magnification75000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION3.1.4
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND
MODEL FITTINGCoot
INITIAL EULER ASSIGNMENTRELION3.1.4
FINAL EULER ASSIGNMENTRELION3.1.4
CLASSIFICATIONRELION3.1.4
RECONSTRUCTIONRELION3.1.4
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION142247