7Q5R
Protein community member pyruvate dehydrogenase complex E2 core from C. thermophilum
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 27.2358 |
| f_angle_d | 0.9184 |
| f_chiral_restr | 0.0677 |
| f_bond_d | 0.0061 |
| f_plane_restr | 0.0047 |
| Sample |
|---|
| Native 60-mer core of Pyruvate Dehydrogenase Complex |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | For plunging, blot force 0 and blotting time of 4 sec were applied. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 7825 |
| Reported Resolution (Å) | 3.84 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial models were predicted using AlphaFold v2.0.1, fitted into reconstructions using COOT and finally refined in real space using COOT and phenix.r ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | FEI FALCON III (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 30 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS GLACIOS |
| Minimum Defocus (nm) | 800 |
| Maximum Defocus (nm) | 2000 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | 2.7 |
| Imaging Mode | BRIGHT FIELD |
| Specimen Holder Model | OTHER |
| Nominal Magnification | 92000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.1 |
| IMAGE ACQUISITION | EPU | 2.9 |
| CTF CORRECTION | cryoSPARC | 3.1 |
| MODEL FITTING | Coot | 0.9.2-pre |
| CLASSIFICATION | cryoSPARC | 3.1 |
| RECONSTRUCTION | cryoSPARC | 3.1 |
| MODEL REFINEMENT | Coot | 0.9.2-pre |
| MODEL REFINEMENT | PHENIX | 1.18.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 276399 | |||
