7PEM
Cryo-EM structure of phophorylated Drs2p-Cdc50p in a PS and ATP-bound E2P state
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 22.3046 |
| f_angle_d | 0.4411 |
| f_chiral_restr | 0.0399 |
| f_plane_restr | 0.0029 |
| f_bond_d | 0.0018 |
| Sample |
|---|
| Binary complex of Drs2p-Cdc50p with the regulatory lipid PI4P and transport substrate PS |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Incubated with 0.1 mg/mL POPS for 1 hour. 3mM ATP was added to the sample just before application to the grid. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 91415 |
| Reported Resolution (Å) | 3.1 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | non-uniform refinement in cryoSPARC v3 |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6ROJ) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | |||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | 69.1 | ||||
| Fitting Procedure | |||||
| Details | Molecular dynamics flexible fitting and energy minimization in Gromacs | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 2 |
| IMAGE ACQUISITION | EPU | |
| CTF CORRECTION | cryoSPARC | 2 |
| MODEL FITTING | PyMOL | |
| MODEL FITTING | Coot | |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 3 |
| CLASSIFICATION | cryoSPARC | 2 |
| RECONSTRUCTION | cryoSPARC | 3 |
| MODEL REFINEMENT | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 3029402 | |||
