Joint neutron/x-ray structure of urate oxidase in complex with 8-hydroxyxanthine
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 | 58.67 |
Crystal Data
Unit Cell |
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Length ( Å ) | Angle ( ˚ ) |
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a = 80.18 | α = 90 |
b = 96.26 | β = 90 |
c = 105.51 | 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 | 2008-10-28 | 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 | 3.25-4.15 | | |
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 | 2 | 20 | 98.5 | 0.04 | | | | | | 23.56 | | | | | | |
2 | 2.3 | 40.06 | 72.2 | 0.133 | | | | | | 7.9 | | 13179 | 13179 | | | |
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 | 2 | 2.14 | | 0.145 | | | | | | 9.54 | | |
2 | 2.3 | 2.42 | | 0.19 | | | | | | 2.2 | | 1328 |
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 | | 2.023 | 19.209 | | 1.99 | | 26344 | 1317 | 97.64 | | 0.1678 | 0.1666 | 0.1887 | | 19.13 |
NEUTRON DIFFRACTION | | 2.298 | 40.067 | | | | 13174 | 663 | 71.08 | | 0.2601 | 0.2586 | 0.2884 | | |
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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15.7423 | | | 5.5013 | | 1.3615 |
14.5584 | | | 7.9063 | | 6.4684 |
RMS Deviations |
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Key | Refinement Restraint Deviation |
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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 |
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Non-Hydrogen Atoms | Number |
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Protein Atoms | 2328 |
Nucleic Acid Atoms | |
Solvent Atoms | 187 |
Heterogen Atoms | 14 |
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 |