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V/A-ATPase from Thermus thermophilus, the soluble domain, including V1, d, two EG stalks, and N-terminal domain of a-subunit.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5Y5Y
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.38 f_angle_d 0.65 f_chiral_restr 0.046 f_bond_d 0.006 f_plane_restr 0.005
Sample Soluble domain of V/A-ATPase including V1, d, two EG stalks, and N-terminal of a-subunit
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK IV Cryogen Name ETHANE Sample Vitrification Details
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 71196 Reported Resolution (Å) 3.5 Resolution Method FSC 0.143 CUT-OFF Other Details Focused classification on the soluble domain was carried out using RELION progarm. Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (5Y5Y) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target Correlation coefficient Overall B Value Fitting Procedure Details
Data Acquisition Detector Type FEI FALCON II (4k x 4k) Electron Dose (electrons/Å**2) 45
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 Nominal Magnification 75000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 300 Imaging Details
EM Software Task Software Package Version IMAGE ACQUISITION EPU CTF CORRECTION Gctf MODEL FITTING Coot INITIAL EULER ASSIGNMENT RELION FINAL EULER ASSIGNMENT RELION CLASSIFICATION RELION RECONSTRUCTION RELION MODEL REFINEMENT PHENIX
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 350000 The particles selected from manually-selected 3084 micrographs.