Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-21) - improved resolution of a dimer building block form RF-21
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 7JK9 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 10.333 |
| f_angle_d | 0.707 |
| f_chiral_restr | 0.093 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.003 |
| Sample |
|---|
| Dimeric building block (RD-21) of the RF-21 oligomeric Chlide:LPOR:NADPH assembly |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | FILAMENT |
| Vitrification Instrument | FEI VITROBOT MARK III |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | HELICAL |
| Number of Particles | 380180 |
| Reported Resolution (Å) | 2.64 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | HELICAL |
| Axial Symmetry | D10 |
| Axial Rise | 153.242 |
| Angular Rotation | 14.6 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (7JK9) | ||||
| 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) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 900 |
| Maximum Defocus (nm) | 2100 |
| 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 | 4.3 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| RECONSTRUCTION | cryoSPARC | 4.3 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||
