5TJ5
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 ... | ||||
| 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 |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 1.3 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND4 | 4.0.17 |
| MODEL FITTING | Coot | 0.8.2 |
| INITIAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.11 |
| RECONSTRUCTION | FREALIGN | 9.11 |
| MODEL REFINEMENT | PHENIX | 1.10.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 657975 | |||
