CryoEM structure of catalytic domain of human HMG-CoA reductase with its inhibitor atorvastatin
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1HWK | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 26.816 |
| r_dihedral_angle_3_deg | 17.151 |
| r_dihedral_angle_6_deg | 15.632 |
| r_lrange_it | 12.382 |
| r_lrange_other | 12.382 |
| r_scangle_it | 10.94 |
| r_scangle_other | 10.937 |
| r_scbond_it | 7.895 |
| r_scbond_other | 7.892 |
| r_mcangle_other | 7.447 |
| Sample |
|---|
| Catalytic part of hHMGCoA reductase |
| 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 | 404712 |
| Reported Resolution (Å) | 2.26 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1hwk) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 42 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | 0.2.4 |
| IMAGE ACQUISITION | EPU | 3.5 |
| CTF CORRECTION | RELION | 4.0 |
| MODEL FITTING | Coot | 0.8.9 |
| INITIAL EULER ASSIGNMENT | RELION | 4.0 |
| FINAL EULER ASSIGNMENT | RELION | 4.0 |
| CLASSIFICATION | RELION | 4.0 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | REFMAC | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3061130 | |||
