Cryo-EM Structure of NADH reduced form of NAD+-dependent Formate Dehydrogenase from Rhodobacter capsulatus
ELECTRON MICROSCOPY
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 14.254 |
| f_angle_d | 0.775 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.01 |
| f_plane_restr | 0.003 |
| Sample |
|---|
| Formate dehydrogenase, NADH reduced |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 199229 |
| Reported Resolution (Å) | 3.24 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C2 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1FDO, 3IAM, 5XF9) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | BACKBONE TRACE | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K2 SUMMIT (4k x 4k) | GATAN K2 SUMMIT (4k x 4k) | |||||||
| Electron Dose (electrons/Å**2) | 64 | 40 | |||||||
| Imaging Experiment | 1 | 2 |
|---|---|---|
| Date of Experiment | ||
| Temperature (Kelvin) | ||
| Microscope Model | FEI POLARA 300 | FEI TITAN KRIOS |
| Minimum Defocus (nm) | ||
| Maximum Defocus (nm) | ||
| Minimum Tilt Angle (degrees) | ||
| Maximum Tilt Angle (degrees) | ||
| Nominal CS | ||
| Imaging Mode | BRIGHT FIELD | BRIGHT FIELD |
| Specimen Holder Model | ||
| Nominal Magnification | ||
| Calibrated Magnification | ||
| Source | FIELD EMISSION GUN | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| CTF CORRECTION | CTFFIND | 4.1.10 |
| MODEL FITTING | Coot | 0.8 |
| INITIAL EULER ASSIGNMENT | IMAGIC | |
| FINAL EULER ASSIGNMENT | RELION | 3.0 |
| RECONSTRUCTION | RELION | 3.0 |
| MODEL REFINEMENT | PHENIX | 1.14 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | CTFFIND4 was used to estimate contrast transfer function parameters. CTF correction was done in Relion 3.0. | |||
