Photosynthetic A10B10 glyceraldehyde-3-phospahte dehydrogenase from Spinacia oleracea.
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 2PKQ | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.444 |
| f_angle_d | 0.678 |
| f_chiral_restr | 0.047 |
| f_plane_restr | 0.005 |
| f_bond_d | 0.004 |
| Sample |
|---|
| A10B10 glyceraldehyde-3-phospahte dehydrogenase hetero-icosamer complexed with NAD. |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Vitrification carried out in conventional atmosphere. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 26638 |
| Reported Resolution (Å) | 7.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | RELION was used for the reconstruction. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C5 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (2PKQ) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | Cross-correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial local fitting was done suing ChimeraX starting from the crystallographic model PDB ID 2PKQ. Refinement was obtained trough several iterative c ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON IV (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1500 |
| Maximum Defocus (nm) | 3000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | Preliminary grid screening was performed on a FEI Tecnai G2 F20 TEM equipped with cryo-box and direct electron detector. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0 |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | 4.1 |
| MODEL FITTING | UCSF ChimeraX | 1.7 |
| RECONSTRUCTION | RELION | 4.0 |
| MODEL REFINEMENT | PHENIX | 1.20 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 3156722 | |||
