6TQL
Cryo-EM of elastase-treated human uromodulin (UMOD)/Tamm-Horsfall protein (THP) filament
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6TQK | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 10.9562 |
| f_angle_d | 0.5633 |
| f_chiral_restr | 0.045 |
| f_bond_d | 0.0031 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Uromodulin (UMOD)/Tamm-Horsfall protein (THP) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 94937 |
| Reported Resolution (Å) | 3.96 |
| Resolution Method | OTHER |
| Other Details | PHENIX ResolveCryoEM FSCref=0.5 |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | C1 |
| Axial Rise | 62.7 |
| Angular Rotation | -179.9 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6TQK, 6TQK, 6TQK) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 171 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45 | ||||||||
| 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 | 165000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 3.0.5 |
| IMAGE ACQUISITION | EPU | 2.4 |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | UCSF Chimera | 1.13 |
| MODEL FITTING | Coot | 0.9 |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | 3.0.5 |
| FINAL EULER ASSIGNMENT | RELION | 3.0.5 |
| CLASSIFICATION | RELION | 3.0.5 |
| RECONSTRUCTION | RELION | 3.0.5 |
| RECONSTRUCTION | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 252438 | |||
