3PLI
Urate oxidase under 1.8 MPa / 18 bars pressure of equimolar mixture xenon : nitrous oxide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2IBA | PDB entry 2IBA |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH | 8.5 | 298 | 10-15 mg.ml-1 urate oxidase; 2mg.ml-1 8-azaxanthine ; 50 mM Tris/HCl pH 8.5; 5-8 % PEG 8000 ; 0-0.05 M NaCl., BATCH, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.98 | 58.76 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 80.294 | α = 90 |
b = 96.27 | β = 90 |
c = 105.513 | γ = 90 |
Symmetry | |
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Space Group | I 2 2 2 |
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 | 298 | IMAGE PLATE | MAR scanner 345 mm plate | Mirrors | 2008-12-04 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM14 | 1.0 | ESRF | BM14 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | 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 | 1.68 | 30 | 98.7 | 0.042 | 34.3 | 4.7 | 46276 | 1 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.68 | 1.74 | 98.2 | 0.247 | 5.1 | 4.3 | 4561 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | 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 | RIGID BODY | THROUGHOUT | PDB entry 2IBA | 1.68 | 14.89 | 43878 | 2341 | 98.77 | 0.16706 | 0.16623 | 0.18278 | RANDOM | 20.717 |
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] | |
0.01 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.035 |
r_dihedral_angle_3_deg | 12.146 |
r_dihedral_angle_4_deg | 9.345 |
r_dihedral_angle_1_deg | 5.887 |
r_scangle_it | 4.337 |
r_scbond_it | 2.542 |
r_mcangle_it | 1.72 |
r_angle_refined_deg | 1.38 |
r_mcbond_it | 0.891 |
r_chiral_restr | 0.097 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2362 |
Nucleic Acid Atoms | |
Solvent Atoms | 170 |
Heterogen Atoms | 17 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |