7E5Z
Dehydrogenase holoenzyme
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 20.7035 |
| f_angle_d | 0.8498 |
| f_chiral_restr | 0.1708 |
| f_bond_d | 0.0322 |
| f_plane_restr | 0.0043 |
| Sample |
|---|
| Formate dehydrogenase from Methylobacterium extorquens AM1 (MeFDH1) |
| Sample Components |
| Formate dehydrogenase alpha subunit from Methylobacterium extorquens AM1 (MeFDH1) |
| Formate dehydrogenase beta subunit from Methylobacterium extorquens AM1 (MeFDH1) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot time was for 4 seconds with 0 blot force before plunging. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 260910 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (6TGA) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | Correlation coefficient | ||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | A initial model was from SWISS modeling using 6TGA as a template. Initial local fitting was done using Chimera and then ISOLDE plugged in ChimeraX for ... | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TALOS ARCTICA |
| Minimum Defocus (nm) | 1200 |
| Maximum Defocus (nm) | 2100 |
| 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 | 100000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 200 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| IMAGE ACQUISITION | EPU | |
| MODEL FITTING | ISOLDE | 1.0.1 |
| MODEL FITTING | UCSF Chimera | 1.13.1 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 2.15.0 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 2.15.0 |
| RECONSTRUCTION | cryoSPARC | 2.15.0 |
| MODEL REFINEMENT | PHENIX | 1.19.1 |
| MODEL REFINEMENT | Coot | 0.8.9.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | 1471548 | Topaz picking facilitated particle picking | ||
