7BL1
human complex II-BATS bound to membrane-attached Rab5a-GTP
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_lrange_it | 264.032 |
| r_mcangle_it | 136.303 |
| r_scangle_it | 135.451 |
| r_scbond_it | 86.101 |
| r_mcbond_it | 78.101 |
| r_dihedral_angle_2_deg | 33.74 |
| r_dihedral_angle_4_deg | 17.49 |
| r_dihedral_angle_3_deg | 16.618 |
| r_dihedral_angle_1_deg | 9.059 |
| r_angle_refined_deg | 1.977 |
| Sample |
|---|
| human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) bound to human Rab5a |
| Sample Components |
| human VPS34 complex II (VPS34-VPS15-Beclin1-UVRAG) |
| Ras-related protein Rab-5A |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | FEI VITROBOT MARK I |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot force 20, blot time 6 s |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SUBTOMOGRAM AVERAGING |
| Number of Particles | 26979 |
| Reported Resolution (Å) | 9.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5DFZ, 3MJH, 4DDP, 3IHY) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation | ||||
| Overall B Value | 320 | ||||
| Fitting Procedure | |||||
| Details | An initial model was build with SWISSMODEL. using 5DFZ, 4DDP and 3IHY. This was then fit manually to density while running restrained MD with ISOLDE. ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 2.99 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 2000 |
| Maximum Defocus (nm) | 5000 |
| 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 | 81000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| VOLUME SELECTION | MATLAB | R2016b |
| IMAGE ACQUISITION | SerialEM | 3.8 |
| CTF CORRECTION | NOVACTF | 1.0.0 |
| MODEL FITTING | Coot | 0.9 |
| MODEL FITTING | ISOLDE | 1.1 |
| FINAL EULER ASSIGNMENT | MATLAB | R2016b |
| CLASSIFICATION | MATLAB | R2016b |
| RECONSTRUCTION | RELION | 3.1 |
| MODEL REFINEMENT | REFMAC | 5.8.0272 |
| MODEL REFINEMENT | ISOLDE | 1.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
