ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 6CT0 | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 22.7131 |
| f_angle_d | 1.1134 |
| f_chiral_restr | 0.0595 |
| f_bond_d | 0.0075 |
| f_plane_restr | 0.0061 |
| 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 2 and blotting time of 6 sec were applied. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 29516 |
| Reported Resolution (Å) | 6.9 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | I |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6CT0) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | 103.25 | ||||
| Fitting Procedure | |||||
| Details | The initial model was used to generate our model using MODELLER. This inital model was fitted into the density using ChimeraX and refined in real spac ... | ||||
| 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 | 45000 |
| Calibrated Magnification | 44067 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | Xmipp | 3.0 |
| IMAGE ACQUISITION | EPU | 2.6 |
| IMAGE ACQUISITION | Scipion | 2.0 |
| IMAGE ACQUISITION | RELION | 3.0 |
| IMAGE ACQUISITION | Xmipp | 3 |
| IMAGE ACQUISITION | MotionCorr2 | 2.03 |
| IMAGE ACQUISITION | Gctf | 1.06 |
| CTF CORRECTION | Gctf | 1.06 |
| MODEL FITTING | UCSF Chimera | 0.94 |
| INITIAL EULER ASSIGNMENT | RELION | 3.0 |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| CLASSIFICATION | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| MODEL REFINEMENT | MODELLER | 9.22 |
| MODEL REFINEMENT | PHENIX | 1.18-3845 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 205251 | Automated selection with template derived from manual selection | ||
