5K12
Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 8.742 |
| f_angle_d | 1.203 |
| f_chiral_restr | 0.07 |
| f_bond_d | 0.009 |
| f_plane_restr | 0.008 |
| Sample |
|---|
| Glutamate dehydrogenase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Plunged into liquiq ethane (FEI VITROBOT MARK IV) |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 21818 |
| Reported Resolution (Å) | 1.8 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | The primary map in this entry corresponds to theuncorrected reconstruction. A version sharpened using a B-factor of -90 is provided as additional volu ... |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D3 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1NR7) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 QUANTUM (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 40 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | FEI TITAN KRIOS |
| Minimum Defocus (nm) | 800 |
| 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 | 215000 |
| Calibrated Magnification | 78000 |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | FREALIGN | 9.10 |
| MODEL FITTING | UCSF Chimera | |
| MODEL REFINEMENT | PHENIX | |
| MODEL REFINEMENT | Coot | |
| INITIAL EULER ASSIGNMENT | FREALIGN | 9.10 |
| FINAL EULER ASSIGNMENT | FREALIGN | 9.10 |
| RECONSTRUCTION | FREALIGN | 9.10 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | 45388 | |||
