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 |