Serial electron diffraction (SerialED) structure of Y122F mutant Ribonucleotide reductase R2 from E. coli in its reduced (red) form
ELECTRON CRYSTALLOGRAPHY
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 1XIK | |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 73.95 | α = 90 |
| b = 76.54 | β = 90 |
| c = 145.74 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 |
Data Collection
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | Mean Isotropic B | |||||
| ELECTRON CRYSTALLOGRAPHY | FREE R-VALUE | 1.8 | 19.93 | 1.34 | 64080 | 1543 | 82.92 | 0.1967 | 0.1961 | 0.2177 | 0.2216 | 0.2349 | 26.54 | ||||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 6.0899 |
| f_angle_d | 0.6976 |
| f_chiral_restr | 0.0402 |
| f_plane_restr | 0.0226 |
| f_bond_d | 0.0043 |
| Sample |
|---|
| Y122F mutant of Ribonucleotide reductase R2 from E. coli in its reduced (red) form |
| Specimen Preparation | |
|---|---|
| Sample Aggregation State | 3D ARRAY |
| Vitrification Instrument | |
| Cryogen Name | ETHANE |
| Sample Vitrification Details | Excess liquid was manually blotted from the backside for approximately 10 seconds, followed by plunge freezing in liquid ethane. Sample was prepared i ... |
| 3D Reconstruction | |
|---|---|
| Reconstruction Method | CRYSTALLOGRAPHY |
| Number of Particles | |
| Reported Resolution (Å) | 1.8 |
| Resolution Method | DIFFRACTION PATTERN/LAYERLINES |
| Other Details | |
| Refinement Type | |
| Symmetry Type | 3D CRYSTAL |
| Space Group Name | |
| Length a | 73.95 |
| Length b | 76.54 |
| Length c | 76.54 |
| Angle Alpha | 90 |
| Angle Beta | 90 |
| Angle Gamma | 90 |
| Map-Model Fitting and Refinement | |||||
|---|---|---|---|---|---|
| Id | 1 (1xik) | ||||
| Refinement Space | RECIPROCAL | ||||
| Refinement Protocol | OTHER | ||||
| Refinement Target | Maximum-likelihood | ||||
| Overall B Value | 26.54 | ||||
| Fitting Procedure | |||||
| Details | |||||
| Data Acquisition | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Detector Type | OTHER | ||||||||
| Electron Dose (electrons/Å**2) | 1.38 | ||||||||
| Imaging Experiment | 1 |
|---|---|
| Date of Experiment | |
| Temperature (Kelvin) | |
| Microscope Model | TFS KRIOS |
| Minimum Defocus (nm) | |
| Maximum Defocus (nm) | 1 |
| Minimum Tilt Angle (degrees) | |
| Maximum Tilt Angle (degrees) | |
| Nominal CS | |
| Imaging Mode | DIFFRACTION |
| Specimen Holder Model | FEI TITAN KRIOS AUTOGRID HOLDER |
| Nominal Magnification | |
| Calibrated Magnification | |
| Source | FIELD EMISSION GUN |
| Acceleration Voltage (kV) | 300 |
| Imaging Details | To address the preferred orientation of ribbon-shaped crystals on the grid, SerialED data was collected at tilt angles of 0, 10, 25, 45, and 60 degrees. Lower tilts minimized absorption for improved resolution, while higher tilts expanded reciprocal space coverage. |
| EM Software | ||
|---|---|---|
| Task | Software Package | Version |
| MODEL FITTING | PHENIX | 1.20.1-4487 |
| MODEL REFINEMENT | PHENIX | 1.20.1-4487 |
| MOLECULAR REPLACEMENT | PHENIX | |
| RECONSTRUCTION | PHENIX | |
| Image Processing | ||||
|---|---|---|---|---|
| CTF Correction Type | CTF Correction Details | Number of Particles Selected | Particle Selection Details | |
| NONE | ||||
