8P2D
Cryo-EM structure of the dimeric form of the anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP
ELECTRON MICROSCOPY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 8P2C | |
Refinement
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 12.077 |
| f_angle_d | 0.48 |
| f_chiral_restr | 0.042 |
| f_plane_restr | 0.003 |
| f_bond_d | 0.002 |
| Sample |
|---|
| Anaerobic ribonucleotide reductase from Prevotella copri produced in the presence of dATP and CTP |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | PARTICLE |
| Vitrification Instrument | FEI VITROBOT MARK IV |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | blot force 1, 5s blot time |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | SINGLE PARTICLE |
| Number of Particles | 1132695 |
| Reported Resolution (Å) | 2.59 |
| Resolution Method | FSC 0.143 CUT-OFF |
| Other Details | |
| Refinement Type | |
| Symmetry Type | POINT |
| Point Symmetry | C1 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (8P2C) | ||||
| Refinement Space | REAL | ||||
| Refinement Protocol | FLEXIBLE FIT | ||||
| Refinement Target | correlation coefficient | ||||
| Overall B Value | 45 | ||||
| Fitting Procedure | |||||
| Details | Manual fitting was done using Coot and automatic real space refinement used phenix.refine | ||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | GATAN K3 (6k x 4k) | ||||||||
| Electron Dose (electrons/Å**2) | 38 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | 600 |
| Maximum Defocus (nm) | 2000 |
| 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 | 105000 |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| PARTICLE SELECTION | cryoSPARC | 3.2.0 |
| IMAGE ACQUISITION | EPU | 2.8.1 |
| CTF CORRECTION | cryoSPARC | 3.2.0 |
| MODEL FITTING | Coot | 0.9.8.7 |
| MODEL REFINEMENT | PHENIX | 1.19.2-4158 |
| INITIAL EULER ASSIGNMENT | cryoSPARC | 3.3.2 |
| FINAL EULER ASSIGNMENT | cryoSPARC | 4.1.2 |
| CLASSIFICATION | cryoSPARC | 4.1.2 |
| RECONSTRUCTION | cryoSPARC | 4.1.2 |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| PHASE FLIPPING AND AMPLITUDE CORRECTION | Patch CTF correction in cryoSPARC | 5762760 | ||
