3J0J
Fitted atomic models of Thermus thermophilus V-ATPase subunits into cryo-EM map
ELECTRON MICROSCOPY
| 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 | ||||
