5VN6
Crystal structure of Taurine dioxygenase from Burkholderia ambifaria
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 7.65 | 290 | RigakuReagents JCSG+ screen, D6: 18% PEG 8000, 100mM Tris base/HCl pH 7.65, 200mM MgCl2: BuamA.00024.a.B1.PS02503 at 20.9mg/ml : cryo: 20% EG: tray 267365D6, puck PRV7-6 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.35 | 47.71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 81.18 | α = 90 |
| b = 84.89 | β = 110.53 |
| c = 95.68 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | C 1 2 1 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 100 | CCD | RAYONIX MX-300 | 2016-02-03 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.97872 | APS | 21-ID-F |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||
| 1 | 2.1 | 40.465 | 99.7 | 0.048 | 0.055 | 0.999 | 19.4 | 4.21 | 35488 | -3 | 36.43 | ||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 2.1 | 2.15 | 99.9 | 0.569 | 0.652 | 0.836 | 2.82 | 4.252 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | PDB entry 3pvj | 2.1 | 40.465 | 1.35 | 35477 | 1978 | 99.81 | 0.167 | 0.1647 | 0.2047 | 51.1444 | ||||||
| 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 | 14.411 |
| f_angle_d | 0.888 |
| f_chiral_restr | 0.056 |
| f_bond_d | 0.007 |
| f_plane_restr | 0.007 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 4188 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 290 |
| Heterogen Atoms | 2 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| XDS | data reduction |
| XSCALE | data scaling |
| MOLREP | phasing |
| PHENIX | model building |
| ARP | model building |
| Coot | model building |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| COMO | phasing |
