8XCZ
Cryo-EM structure of glutamate dehydrogenase from thermococcus profundus incorporating NADP and GLU in the steady stage of reaction
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 3.45 |
| f_angle_d | 0.394 |
| f_chiral_restr | 0.041 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Hexamer of glutamate dehydrogenase in the presence of NADP and glutamate |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | The sample solution kept at room temperature was flash-frozen 1-h after mixing GDH, NADP and glutamate solutions. |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 168650 |
| Reported Resolution (Å) | 2.83 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 | ||||
| Refinement Space | |||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 1 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | JEOL CRYO ARM 300 |
| Minimum Defocus (nm) | 400 |
| Maximum Defocus (nm) | 47000 |
| 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 | Grid information as following: Company/model: Quantifoil Cu 1.2/1.3 Material:Cu Grid mesh: 200 |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | RELION | 4.0beta |
| IMAGE ACQUISITION | SerialEM | |
| CTF CORRECTION | CTFFIND | |
| MODEL FITTING | Coot | |
| MODEL REFINEMENT | PHENIX | |
| INITIAL EULER ASSIGNMENT | RELION | 4.0beta |
| FINAL EULER ASSIGNMENT | RELION | 4.0beta |
| CLASSIFICATION | RELION | 4.0beta |
| RECONSTRUCTION | RELION | 4.0beta |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 6334528 | Auto-picking based on templates from manually picked GDH particles. | ||
