Joint neutron/X-ray structure of urate oxidase in complex with 8-azaxanthine
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | temperature-controlled batch | 8.5 | 291 | 5 % PEG 8000, 0.1 M NaCl, 0.1 M TrisHCl pD 8.5, 8 mg/ml urate oxidase, temperature-controlled batch, temperature 291K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.98 | 58.71 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 80.2 | α = 90 |
| b = 96.2 | β = 90 |
| c = 105.5 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | I 2 2 2 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 293 | IMAGE PLATE | MAR scanner 345 mm plate | Xenocs | 2008-04-28 | M | SINGLE WAVELENGTH | |||||
| 2 | 1 | neutron | 293 | IMAGE PLATE | CUSTOM-MADE | 2008-08-30 | L | LAUE | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SEALED TUBE | OTHER | 1.54 | ||
| 2 | NUCLEAR REACTOR | OTHER | 3.25-4.35 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | R Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | 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 | 1.9 | 61.43 | 73.2 | 0.141 | 9.2 | 23362 | 23362 | ||||||||||||
| 2 | 1.92 | 50 | 96.5 | 0.042 | 19.88 | ||||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | R Merge I (Observed) | R-Sym I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | R Split (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||
| 1 | 1.9 | 2 | 0.236 | 2.6 | |||||||||||||||
| 2 | 1.92 | 2.04 | 0.144 | 8.53 | |||||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | ||
| X-RAY DIFFRACTION | 1.919 | 33.029 | 1.99 | 30380 | 1519 | 96.25 | 0.1414 | 0.1398 | 0.14 | 0.1723 | 0.174 | 24.41 | |||||||
| NEUTRON DIFFRACTION | 1.904 | 48.1 | 23199 | 1139 | 71.8 | 0.2412 | 0.2398 | 0.2672 | |||||||||||
| 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 | 19.432 |
| f_angle_d | 1.485 |
| f_chiral_restr | 0.104 |
| f_bond_d | 0.014 |
| f_plane_restr | 0.008 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2309 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 169 |
| Heterogen Atoms | 13 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| LADI-III | data collection |
| MOLREP | phasing |
| PHENIX | refinement |
| LAUEGEN | data reduction |
| SCALA | data scaling |
