8AVC
Mouse leptin:LEP-R complex cryoEM structure (3:3 model)
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 5.364 |
| f_angle_d | 0.7721 |
| f_chiral_restr | 0.0524 |
| f_plane_restr | 0.0052 |
| f_bond_d | 0.0035 |
| Sample |
|---|
| Stucture of mouse leptin in complex with a trimerized form of the mouse Lep-R extracellular region |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | LEICA EM GP |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 37530 |
| Reported Resolution (Å) | 4.6 |
| 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 | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 2500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | OTHER |
| Specimen Holder Model | |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | v3.3.1 |
| CTF CORRECTION | cryoSPARC | v3.3.1 |
| MODEL FITTING | UCSF Chimera | 1.17 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | v3.3.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | v3.3.1 |
| CLASSIFICATION | cryoSPARC | v3.3.1 |
| RECONSTRUCTION | cryoSPARC | v3.3.1 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 141157 | Movies were processed via patch-based motion correction and CTF estimation as implemented in cryoSPARC v3.3.1. Initial 2D classes were obtained by the blob picker function in cryoSPARC, followed by particle picking via TOPAZ as implemented in cryoSPARC. Junk particles were removed by multiple rounds of 2D classification and ab initio 3D classification resulting in a particle set of 141,157 particles. | ||
