3LD4
Urate oxidase complexed with 8-nitro xanthine
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 | BATCH | 8 | 291 | 0.05M TRIS BUFFER PH 8, 8% PEG 8000, 0.02M NACL , BATCH, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.91 | 57.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 78.582 | α = 90 |
b = 95.045 | β = 90 |
c = 104.371 | 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 | CCD | ADSC QUANTUM 315r | CURVATED MIRRORS | 2007-05-03 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE BM30A | 0.964 | ESRF | BM30A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 1.35 | 29.4 | 99.4 | 0.046 | 0.044 | 25 | 7.6 | 87363 | 81256 | 2 | 4 | 15 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 1.35 | 1.42 | 99.4 | 0.164 | 0.16 | 4.4 | 4.5 | 11863 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation 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 (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | AB INITIO | THROUGHOUT | 3L8W | 1.35 | 10 | 4 | 85679 | 80616 | 3978 | 99.4 | 0.192 | 0.185 | 0.182 | 0.225 | RANDOM |
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 |
9 | 2313 | 2648.5 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
s_non_zero_chiral_vol | 0.076 |
s_anti_bump_dis_restr | 0.074 |
s_angle_d | 0.072 |
s_zero_chiral_vol | 0.065 |
s_similar_adp_cmpnt | 0.05 |
s_from_restr_planes | 0.0301 |
s_bond_d | 0.027 |
s_similar_dist | |
s_rigid_bond_adp_cmpnt | |
s_approx_iso_adps |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2363 |
Nucleic Acid Atoms | |
Solvent Atoms | 265 |
Heterogen Atoms | 19 |
Software
Software | |
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Software Name | Purpose |
ADSC | data collection |
SHELX | model building |
SHELXL-97 | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
SHELX | phasing |