PSI complex of A.thaliana isolated using DOC based Clear-Native-PAGE method
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8J7B | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| s_dihedral_angle_6_deg | 15.1713 |
| s_dihedral_angle_3_deg | 12.0455 |
| s_dihedral_angle_1_deg | 6.5315 |
| s_dihedral_angle_2_deg | 3.5484 |
| s_angle_nonh_deg | 2.0721 |
| s_nbtor | 0.2373 |
| s_nbd | 0.2201 |
| s_hbond_nbd | 0.1612 |
| s_chiral_restr | 0.0999 |
| s_bond_nonh_d | 0.0196 |
| Sample |
|---|
| PSI complex of A.thaliana isolated DOC based Clear-Native-PAGE method |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 148985 |
| Reported Resolution (Å) | 2.18 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8J7B) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | 40.0832 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 500 |
| Maximum Defocus (nm) | 1500 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 0.01 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Topaz | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.9 |
| MODEL FITTING | Coot | 0.9.8.7 |
| INITIAL EULER ASSIGNMENT | RELION | 4.0.2 |
| FINAL EULER ASSIGNMENT | RELION | 4.0.2 |
| CLASSIFICATION | RELION | 4.0.2 |
| RECONSTRUCTION | RELION | 4.0.2 |
| MODEL REFINEMENT | Servalcat | 0.4.115 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING ONLY | 1629453 | |||
