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Reconstituted yeast V-ATPase bound to Rtc5p
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FDA in silico model AlphaFold
Refinement RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 7.0236 f_angle_d 0.6138 f_chiral_restr 0.04 f_bond_d 0.0054 f_plane_restr 0.0047
Sample Reconstituted yeast V-ATPase bound to Rtc5p
Specimen Preparation Sample Aggregation State PARTICLE Vitrification Instrument LEICA EM GP Cryogen Name ETHANE Sample Vitrification Details Leica EM GP2
3D Reconstruction Reconstruction Method SINGLE PARTICLE Number of Particles 90977 Reported Resolution (Å) 3.6 Resolution Method FSC 0.143 CUT-OFF Other Details Refinement Type Symmetry Type POINT Point Symmetry C1
Map-Model Fitting and Refinement Id 1 (7fda) Refinement Space Refinement Protocol Refinement Target Overall B Value Fitting Procedure Details
Data Acquisition Detector Type TFS FALCON 4i (4k x 4k) Electron Dose (electrons/Å**2) 52.5
Imaging Experiment 1 Date of Experiment Temperature (Kelvin) Microscope Model TFS GLACIOS Minimum Defocus (nm) 400 Maximum Defocus (nm) 2000 Minimum Tilt Angle (degrees) Maximum Tilt Angle (degrees) Nominal CS 2.7 Imaging Mode BRIGHT FIELD Specimen Holder Model Nominal Magnification 92000 Calibrated Magnification Source FIELD EMISSION GUN Acceleration Voltage (kV) 200 Imaging Details
EM Software Task Software Package Version PARTICLE SELECTION Topaz CTF CORRECTION CTFFIND 4.1.14 MODEL FITTING Coot MODEL FITTING ISOLDE INITIAL EULER ASSIGNMENT RELION 5 FINAL EULER ASSIGNMENT RELION 5 RECONSTRUCTION RELION 5 MODEL REFINEMENT PHENIX 1.21_5207
Image Processing CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details PHASE FLIPPING AND AMPLITUDE CORRECTION 332570