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 8R1O | pdb_00008r1o

Structure of C. thermophilum RNA exosome core


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelModeller 
in silico modelAlphaFoldAF-G0S755-F1,AF-G0SC21-F1,AF-G0S1P1-F1,AF-G0SCD1-F1,AF-G0RZG4-F1,AF-P0CT46-F1,AF-G0RZX8-F1,AF-G0S9A0-F1,AF-G0SE33-F1 
Sample
RNA exosome core (Exo9)
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsSample volume 3 ul Wait time 5 s, Blot time 5 s, Delay time 0 s Force 12
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles276958
Reported Resolution (Å)3.19
Resolution MethodFSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry TypePOINT
Map-Model Fitting and Refinement
Id1
Refinement SpaceREAL
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeGATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelJEOL CRYO ARM 200
Minimum Defocus (nm)600
Maximum Defocus (nm)2200
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelJEOL CRYOSPECPORTER
Nominal Magnification60000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION4.0.1
IMAGE ACQUISITIONSerialEM
CTF CORRECTIONRELION4.0.1
CTF CORRECTIONCTFFIND4.1
MODEL FITTINGUCSF ChimeraX1.1
MODEL FITTINGPHENIX1.20.1-4487
MODEL REFINEMENTPHENIX1.20.1-4487
MODEL REFINEMENTISOLDE1.6
MODEL REFINEMENTCoot0.9.6
INITIAL EULER ASSIGNMENTRELION4.0.1
FINAL EULER ASSIGNMENTRELION4.0.1
CLASSIFICATIONRELION4.0.1
RECONSTRUCTIONRELION4.0.1
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION2448810