9DYG | pdb_00009dyg

iSAT-PNA-RA20, RA20-B-c class


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YBB 
experimental modelPDB 8RPY 
Sample
iSAT-PNA-RA20 50S ribosomal subunit assembly intermediate
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details3 microliter of the sample was added.
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles9000
Reported Resolution (Å)5.27
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1 (4YBB, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY, 8RPY)
Refinement SpaceREAL
Refinement ProtocolOTHER
Refinement TargetComprehensive validation (cryo-EM)
Overall B Value120.42
Fitting Procedure
DetailsThe atomic model was fitted into a low resolution (5 Angstrom) EM map; therefore the coordinates should only serve as a general visual representation ...The atomic model was fitted into a low resolution (5 Angstrom) EM map; therefore the coordinates should only serve as a general visual representation and should not be looked into detail. Initial docking of the atomic model was done in ChimeraX. Coot and Phenix were used for real-space refinements. Geometry minimization in Phenix was used to improve the RNA atomic model.
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)25.4
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)1000
Maximum Defocus (nm)2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging ModeBRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARC
IMAGE ACQUISITIONLeginon
MODEL FITTINGUCSF ChimeraX
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
NONECTF correction were performed by Patch CTF Estimation of cryoSPARC