3JD3
Glutamate dehydrogenase in complex with NADH and GTP, open conformation
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.461 |
| f_angle_d | 1.086 |
| f_chiral_restr | 0.379 |
| f_bond_d | 0.01 |
| f_plane_restr | 0.004 |
| Sample |
|---|
| Ternary complex of bovine glutamate dehydrogenase with GTP and NADH |
| Sample Components |
| L-glutamate:NAD(P)+ oxidoreductase (deaminating) |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Blot for 3-6 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 14793 |
| Reported Resolution (Å) | 3.6 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | (Single particle--Applied symmetry: D3) |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (3MW9) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | REFINEMENT PROTOCOL--flexible | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 45 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | 2014-07-27 |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 1000 |
| Maximum Defocus (nm) | 5000 |
| 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 | 78426 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | CTFFIND | 3 |
| MODEL FITTING | Coot | |
| MODEL FITTING | PHENIX | |
| MODEL FITTING | Rosetta | |
| MODEL FITTING | UCSF Chimera | |
| RECONSTRUCTION | EMAN | 2 |
| RECONSTRUCTION | RELION | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| Each micrograph | ||||
