Joint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine
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 | 58.67 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 80.18 | α = 90 |
| b = 96.26 | β = 90 |
| c = 105.51 | 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 | 2008-10-28 | 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 | 3.25-4.15 | ||
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 | 2 | 20 | 98.5 | 0.04 | 23.56 | ||||||||||||||
| 2 | 2.3 | 40.06 | 72.2 | 0.133 | 7.9 | 13179 | 13179 | ||||||||||||
| 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 | 2 | 2.14 | 0.145 | 9.54 | |||||||||||||||
| 2 | 2.3 | 2.42 | 0.19 | 2.2 | 1328 | ||||||||||||||
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 | 2.023 | 19.209 | 1.99 | 26344 | 1317 | 97.64 | 0.1678 | 0.1666 | 0.1648 | 0.1887 | 0.1843 | 19.13 | |||||||
| NEUTRON DIFFRACTION | 2.298 | 40.067 | 13174 | 663 | 71.08 | 0.2601 | 0.2586 | 0.2884 | |||||||||||
| 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] | |
| 15.7423 | 5.5013 | 1.3615 | ||||
| 14.5584 | 7.9063 | 6.4684 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| f_dihedral_angle_d | 16.275 |
| f_angle_d | 2.409 |
| f_bond_d | 0.075 |
| f_chiral_restr | 0.048 |
| f_plane_restr | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2328 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 187 |
| Heterogen Atoms | 14 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| LADI-III | data collection |
| MOLREP | phasing |
| PHENIX | refinement |
| LAUEGEN | data reduction |
| SCALA | data scaling |














