7YCA
Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 18.385 |
| f_angle_d | 1.659 |
| f_chiral_restr | 0.083 |
| f_bond_d | 0.012 |
| f_plane_restr | 0.011 |
| Sample |
|---|
| photosystem I-light-harvesting complex I-prasinophyte-specific Lhc protein (PSI-LHCI-Lhcp) supercomplex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | NITROGEN |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 80366 |
| Reported Resolution (Å) | 2.94 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 5ZJI, 7D0J, 7D0J) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | 110.967 | ||||
| Fitting Procedure | |||||
| Details | Initial local fitting was done using Chimera and then Wincoot was usd for flexible fitting | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 BASE (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 60 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN |
| Minimum Defocus (nm) | 1800 |
| Maximum Defocus (nm) | 2200 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| 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 | 3.3.1 |
| CTF CORRECTION | cryoSPARC | 3.3.1 |
| CTF CORRECTION | MotionCorr2 | 1.3 |
| MODEL FITTING | UCSF Chimera | 1.16 |
| INITIAL EULER ASSIGNMENT | RELION | 3.1 |
| FINAL EULER ASSIGNMENT | RELION | 3.1 |
| RECONSTRUCTION | RELION | 3.1 |
| MODEL REFINEMENT | PHENIX | 1.19.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 5288217 | Template picker was used to automatically select particle images | ||
