8ASV

Cryo-EM structure of yeast Elongator complex


ELECTRON MICROSCOPY

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QK7 
experimental modelPDB 4A8J 
Sample
Yeast Elongator complex
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification Details15 s wait time, blot force 5, 5 s blot time
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles12514
Reported Resolution (Å)4.35
Resolution MethodFSC 0.143 CUT-OFF
Other Details3D auto-refine followed by Post-processing
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (6QK7, 4A8J)
Refinement Space
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsAfter initial rigid body fit, further fitting was done using MDFF and NAMDINATOR
Data Acquisition
Detector TypeGATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)40
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelTFS KRIOS
Minimum Defocus (nm)900
Maximum Defocus (nm)3000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification105000
Calibrated Magnification
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONcryoSPARCv3.2.0
IMAGE ACQUISITIONEPU2.10
CTF CORRECTIONcryoSPARCv3.2.0
MODEL FITTINGUCSF ChimeraX
INITIAL EULER ASSIGNMENTcryoSPARCv3.2.0
FINAL EULER ASSIGNMENTRELION3.1
CLASSIFICATIONRELION3.1
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION188389given number of particles is after TOPAZ picking and 2D cleaning