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Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
6.24
f_angle_d
1.245
f_chiral_restr
0.05
f_bond_d
0.01
f_plane_restr
0.006
Sample
Vo region of the V-ATPase from Saccharomyces cerevisiae
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE-PROPANE
Sample Vitrification Details
Modified for ethane/propane
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
462842
Reported Resolution (Å)
3.9
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Data beyond 6 A resolution were omitted from refinement.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
OTHER
Refinement Target
Overall B Value
Fitting Procedure
Details
phenix.real_space_refine
REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
MODEL TO MAP FIT.
CC(ACROSS WHOLE MAP VOLUME): 0.6772 ...
phenix.real_space_refine
REFINEMENT TARGET: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
MODEL TO MAP FIT.
CC(ACROSS WHOLE MAP VOLUME): 0.6772
CC(ONLY ACROSS ATOMS IN THE MODEL): 0.6842
Data Acquisition
Detector Type
GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å**2)
100
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
Maximum Defocus (nm)
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
37000
Calibrated Magnification
64350
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
70 micro meter objective aperture, illuminated area of 1.58 micro meter diameter