6BF8
Cryo-EM structure of human insulin degrading enzyme in complex with insulin
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.318 |
| f_angle_d | 1.213 |
| f_chiral_restr | 0.064 |
| f_plane_restr | 0.009 |
| f_bond_d | 0.007 |
| Sample |
|---|
| Insulin degrading enzyme |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | HOMEMADE PLUNGER |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | The cryo grids were made using Spotiton |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 110499 |
| Reported Resolution (Å) | 4.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 92 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 7.9 | 6.8 | |||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 940 |
| Maximum Defocus (nm) | 2200 |
| 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 | 22500 |
| Calibrated Magnification | 46598 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | The image was collected at 20-50 degree tilt |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | DoG Picker | |
| IMAGE ACQUISITION | Leginon | 3.3 |
| CTF CORRECTION | Gctf | Gctf-v0.50_sm_30_cu7.5_x86_64 |
| MODEL FITTING | Coot | Coot 0.8.9_pre |
| MODEL FITTING | UCSF Chimera | Chimera 1.11.2 |
| MODEL REFINEMENT | PHENIX | Phenix-1.12-2829 |
| INITIAL EULER ASSIGNMENT | RELION | 2.0 |
| FINAL EULER ASSIGNMENT | RELION | 2.0 |
| CLASSIFICATION | RELION | 2.0 |
| RECONSTRUCTION | RELION | 2.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 762283 | |||
