8J79
Bovine Xanthine Oxidoreductase Crystallized with oxypurinol
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1FO4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | The enzyme solution was exchanged buffer into 50 mM Tris-HCl pH 7.4 and diluted with 50 mM Tris-HCl pH 7.4, 5 mM DTT, 100 micro M oxypurinol, and 30% glycerol to a concentration of 8.6 mg/ml. The precipitant solution contained 50 mM potassium phosphate pH 6.0, 5 mM DTT, 0.2 mM EDTA, 100 micro M oxypurinol, 30% glycerol and 14%-15% PEG 4000. 10 micro L enzyme solution and 10 micro L reservoir solution were mixed on siliconized glass plates and kept in the dark at 20 C for 5 days. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.73 | 54.92 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 167.678 | α = 90 |
b = 123.47 | β = 90.89 |
c = 150.059 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-07-21 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SPRING-8 BEAMLINE BL44XU | 0.9 | SPring-8 | BL44XU |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 1.99 | 48.43 | 99.7 | 0.996 | 10.6 | 5 | 210046 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.99 | 2.11 | 0.843 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 1.99 | 47.72 | 199435 | 10629 | 99.74 | 0.16515 | 0.16346 | 0.19667 | RANDOM | 29.898 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.823 |
r_dihedral_angle_4_deg | 15.529 |
r_dihedral_angle_3_deg | 13.276 |
r_dihedral_angle_1_deg | 6.975 |
r_long_range_B_refined | 5.806 |
r_long_range_B_other | 5.697 |
r_scangle_other | 4.54 |
r_scbond_it | 3.095 |
r_scbond_other | 3.095 |
r_mcangle_it | 3.065 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 19980 |
Nucleic Acid Atoms | |
Solvent Atoms | 1815 |
Heterogen Atoms | 248 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XDS | data scaling |
MOLREP | phasing |