Glycerol dehydrogenase
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8X6M | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 4.615 |
| f_angle_d | 0.548 |
| f_chiral_restr | 0.043 |
| f_plane_restr | 0.004 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Glycerol dehydrogenase |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 42688 |
| Reported Resolution (Å) | 3.2 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | Gold-standard half maps were generated in cryoSPARC v4.7.1 during final non-uniform refinement from independently refined half-datasets. |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | D4 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8X6M) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | RIGID BODY FIT | ||||
| Refinement Target | |||||
| Overall B Value | |||||
| Fitting Procedure | |||||
| Details | Initial global fitting was done using ChimeraX and then Coot was used for manual fitting | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | TFS FALCON 4i (4k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 50 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 1750 |
| Maximum Defocus (nm) | 2750 |
| 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 | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 4.7.1 |
| CTF CORRECTION | cryoSPARC | 4.7.1 |
| MODEL FITTING | UCSF ChimeraX | 1.12 |
| MODEL FITTING | Coot | 0.9.8.95 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.7.1 |
| RECONSTRUCTION | cryoSPARC | 4.7.1 |
| MODEL REFINEMENT | PHENIX | 1.21.2_5419 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Initial particles were selected using blob picking. Templates generated from 2D class averages were subsequently used for template-based particle picking in cryoSPARC | 5748338 | ||