3J9T

Yeast V-ATPase state 1


ELECTRON MICROSCOPY
Sample
Vacuolar-type ATPase
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK III
Cryogen NameOTHER
Sample Vitrification DetailsBlot for 23 seconds before freezing in ethane/propane mixture (FEI VITROBOT MARK III).
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles50503
Reported Resolution (Å)6.9
Resolution MethodFSC 0.143 CUT-OFF
Other Details(Single particle details: Particles automatically selected using TMaCS and processed in Relion.) (Single particle--Applied symmetry: C1)
Refinement Type
Symmetry TypePOINT
Point SymmetryC1
Map-Model Fitting and Refinement
Id1 (1U7L, 1HO8, 4RND, 4RND, 4DL0, 4DL0)
Refinement SpaceREAL
Refinement ProtocolFLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
DetailsREFINEMENT PROTOCOL--flexible DETAILS--Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics ...REFINEMENT PROTOCOL--flexible DETAILS--Rigid body fitting performed in Chimera first, followed by flexible fitting performed using Molecular Dynamics Flexible Fitting (MDFF).
Data Acquisition
Detector TypeGATAN K2 (4k x 4k)
Electron Dose (electrons/Å**2)30
Imaging Experiment1
Date of Experiment2013-10-19
Temperature (Kelvin)77
Microscope ModelFEI TECNAI F20
Minimum Defocus (nm)1500
Maximum Defocus (nm)7000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2
Imaging ModeBRIGHT FIELD
Specimen Holder ModelGATAN LIQUID NITROGEN
Nominal Magnification34483
Calibrated Magnification34483
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)200
Imaging DetailsK2 Summit in counting mode, 2 frames/s for 15 s
EM Software
TaskSoftware PackageVersion
MODEL FITTINGMDFF
MODEL FITTINGUCSF Chimera
PARTICLE SELECTIONTMaCS
RECONSTRUCTIONRELION
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
Each particle