Joint neutron/X-ray structure of urate oxidase in complex with 8-azaxanthine
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Crystallization
Crystalization Experiments |
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ID | Method | pH | Temperature | Details |
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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 |
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Matthews coefficient | Solvent content |
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2.98 | 58.71 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 80.2 | α = 90 |
b = 96.2 | β = 90 |
c = 105.5 | γ = 90 |
Symmetry |
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Space Group | I 2 2 2 |
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Diffraction
Diffraction Experiment |
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol |
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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 |
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
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1 | SEALED TUBE | OTHER | 1.54 | | |
2 | NUCLEAR REACTOR | OTHER | 3.25-4.35 | | |
Data Collection
Overall |
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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 |
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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 |
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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) |
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1 | 1.9 | 2 | | 0.236 | | | | | | 2.6 | | |
2 | 1.92 | 2.04 | | 0.144 | | | | | | 8.53 | | |
Refinement
Statistics |
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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 | R-Free | R-Free Selection Details | Mean Isotropic B |
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X-RAY DIFFRACTION | | 1.919 | 33.029 | | 1.99 | | 30380 | 1519 | 96.25 | | 0.1414 | 0.1398 | 0.1723 | | 24.41 |
NEUTRON DIFFRACTION | | 1.904 | 48.1 | | | | 23199 | 1139 | 71.8 | | 0.2412 | 0.2398 | 0.2672 | | |
Temperature Factor Modeling |
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] |
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| | | | | |
| | | | | |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2309 |
Nucleic Acid Atoms | |
Solvent Atoms | 169 |
Heterogen Atoms | 13 |
Software
Software |
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Software Name | Purpose |
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LADI-III | data collection |
MOLREP | phasing |
PHENIX | refinement |
LAUEGEN | data reduction |
SCALA | data scaling |