8JF0
Human sodium-dependent vitamin C transporter 1 in an intermediate state
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8JEZ | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_long_range_B_refined | 49.924 |
| r_long_range_B_other | 49.923 |
| r_dihedral_angle_2_deg | 34.819 |
| r_scangle_other | 25.486 |
| r_mcangle_it | 24.414 |
| r_mcangle_other | 24.409 |
| r_dihedral_angle_4_deg | 17.714 |
| r_scbond_it | 15.047 |
| r_scbond_other | 15.043 |
| r_mcbond_other | 14.672 |
| Sample |
|---|
| Human SVCT1 dimer in an intermediate state |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 149304 |
| Reported Resolution (Å) | 3.5 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8JEZ) | ||||
| Refinement Space | |||||
| Refinement Protocol | |||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 BIOQUANTUM (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50.9 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 1600 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | BRIGHT FIELD |
| 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 | RELION | 3.1.1 |
| IMAGE ACQUISITION | EPU | 1.24.2 |
| CTF CORRECTION | RELION | 3.1.1 |
| MODEL FITTING | Coot | 0.9.6 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1.1 |
| RECONSTRUCTION | RELION | 3.1.1 |
| MODEL REFINEMENT | Servalcat | 0.2.115 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3699304 | |||
