Imidazole glycerol phosphate dehydratase from Mycobacterium tuberculosis, apo structure
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4LPF | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 12.655 |
| r_long_range_B_other | 12.655 |
| r_dihedral_angle_3_deg | 11.205 |
| r_scangle_other | 10.054 |
| r_dihedral_angle_1_deg | 6.265 |
| r_scbond_it | 6.052 |
| r_scbond_other | 6.052 |
| r_mcangle_it | 5.966 |
| r_mcangle_other | 5.966 |
| r_mcbond_it | 4.198 |
| Sample |
|---|
| Mycobacterium tuberculosis HisB,5-bromo-1-propyl-1H-1,2,4-traizole added but not modelled |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 96264 |
| Reported Resolution (Å) | 2.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | O |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (4LPF) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | |||||
| Overall B Value | 103.3 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 26.5 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 12000 |
| Maximum Defocus (nm) | 35000 |
| 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 | 96000 |
| Calibrated Magnification | 166666 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | CTFFIND | 4.1 |
| CTF CORRECTION | RELION | 4.0 |
| MODEL FITTING | UCSF Chimera | 1.18 |
| MODEL FITTING | Coot | 0.9.8.95 |
| INITIAL EULER ASSIGNMENT | RELION | 4.0 |
| FINAL EULER ASSIGNMENT | RELION | 4.0 |
| CLASSIFICATION | RELION | 4.0 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | REFMAC | 5.8.0430 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 150382 | |||
