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Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A5C experimental model PDB 3K5B experimental model PDB 1R5Z
Sample Detergent solubilized membrane protein complex Sample Components Subunit A of V-ATPase Subunit B of V-ATPase Subunit D of V-ATPase Subunit F of V-ATPase Subunit E of V-ATPase Subunit G of V-ATPase Subunit C of V-ATPase
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument FEI VITROBOT MARK III Cryogen Name ETHANE Sample Vitrification Details Vitrification from 4 degree Celsius environment
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 46105 Reported Resolution (Å) 9.7 Resolution Method Other Details Frealign and new software used for refinement and reconstruction Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (3A5C) 2 (3K5B) 3 (1R5Z) Refinement Space REAL Refinement Protocol FLEXIBLE FIT Refinement Target correlation coefficient (UCSF chimera, rigid) and imodfit (flexible) Overall B Value Fitting Procedure Details REFINEMENT PROTOCOL--rigid (subunit A, B, D, F, E, and G) and flexible fitting
(subunit C)
Data Acquisition Detector Type GENERIC FILM Electron Dose (electrons/Å**2) 0.18
Imaging Experiment 1 Date of Experiment 2010-01-01 Temperature (Kelvin) 100 Microscope Model FEI TECNAI F20 Minimum Defocus (nm) 2500 Maximum Defocus (nm) 4500 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 50000 Calibrated Magnification 50000 Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version MODEL FITTING iMODFIT MODEL FITTING UCSF Chimera RECONSTRUCTION Build_Fspace RECONSTRUCTION FREALIGN RECONSTRUCTION Refine_Fspace
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details Each particle