6RGT
Crystal structure of the cofactor-free Aspergillus flavus urate oxidase T57A variant anaerobically complexed with 9-methyl uric acid
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4CW0 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | BATCH MODE | 293 | 20 MG/ML UOX T57A IN 50 MM TRIS-HCL PH 8.0 SATURATED WITH 9-METHYL URIC ACID, 8% PEG 8000 - CRYSTALS GROWN ANAEROBICALLY |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.88 | 57.23 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 79.291 | α = 90 |
b = 95.116 | β = 90 |
c = 104.503 | 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 | OXFORD SAPPHIRE CCD | 2017-06-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SEALED TUBE | OXFORD DIFFRACTION NOVA | 1.54 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.6 | 14.02 | 99.8 | 0.104 | 0.117 | 0.051 | 0.996 | 9.3 | 4.9 | 52248 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.6 | 1.69 | 99.7 | 1.411 | 1.738 | 0.991 | 0.361 | 0.9 | 3 |
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 | FOURIER SYNTHESIS | THROUGHOUT | 4CW0 | 1.6 | 14.02 | 49561 | 2683 | 99.68 | 0.16295 | 0.16152 | 0.18905 | RANDOM | 17.011 |
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] | |
1.6 | -0.57 | -1.03 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.089 |
r_dihedral_angle_4_deg | 15.705 |
r_dihedral_angle_3_deg | 12.634 |
r_long_range_B_refined | 7.663 |
r_dihedral_angle_1_deg | 7.166 |
r_long_range_B_other | 6.49 |
r_scangle_other | 3.272 |
r_mcangle_it | 2.903 |
r_mcangle_other | 2.903 |
r_scbond_it | 2.053 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2404 |
Nucleic Acid Atoms | |
Solvent Atoms | 597 |
Heterogen Atoms | 37 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
CrysalisPro | data reduction |
Aimless | data scaling |
REFMAC | phasing |