4POE
Urate oxidase co-crystallized with uric acid and azide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3L8W |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 8.5 | 291 | MIXING TWO SOLUTIONS A AND B: SOLUTION A: PROTEIN AT 20MG/ML IN 50MM TRIS-ACETATE BUFFER, + 0.3M SODIUM AZIDE SATURATED BY URIC ACID (IN PRESENCE OF THE SOLID), PH 8.5 SOLUTION B: PEG-8000 18% IN TRIS BUFFER, BATCH METHOD, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.81 | 57.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.524 | α = 90 |
b = 95.24 | β = 90 |
c = 104.577 | 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 | 100 | PIXEL | DECTRIS PILATUS 6M | BENT MIRROR | 2014-01-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID23-1 | ESRF | ID23-1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge 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 | 1.05 | 47.6 | 99.3 | 0.068 | 4.4 | 148909 | 2 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 1.05 | 1.12 | 54.8 | 0.325 | 2 | 3.15 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | FOURIER SYNTHESIS | 3L8W | 1.07 | 47 | 4 | 172500 | 148909 | 85.7 | 0.185 | 0.185 |
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] | |
Coordinate Error | ||
---|---|---|
Structure Solution Method | Refinement High Resolution | Refinement Low Resolution |
4 | 2299 | 2669.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_from_restr_planes | 0.406 |
s_non_zero_chiral_vol | 0.092 |
s_approx_iso_adps | 0.088 |
s_anti_bump_dis_restr | 0.082 |
s_angle_d | 0.076 |
s_zero_chiral_vol | 0.075 |
s_similar_adp_cmpnt | 0.038 |
s_bond_d | 0.03 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2362 |
Nucleic Acid Atoms | |
Solvent Atoms | 308 |
Heterogen Atoms | 7 |
Software
Software | |
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Software Name | Purpose |
DNA | data collection |
SHELX | model building |
SHELXL-97 | refinement |
XDS | data reduction |
SCALA | data scaling |
TRUNCATE | data scaling |
SHELX | phasing |