4D13 | pdb_00004d13

Crystal structure of cofactor-free urate oxidase in complex with its 5-peroxoisourate intermediate (X-ray dose, 2.2 kGy)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1820MG/ML UOX IN 50 MM TRIS-ACETATE PH 8.0 SATURATED WITH 9-METHYL URIC ACID UNDER ANAEROBIC CONDITIONS RESERVOIR: 8% PEG 8000, 50 MM TRIS-ACETATE PH 8.0 CRYSTALLIZATION WAS CARRIED OUT ANAEROBICALLY. CRYSTALS WERE INCUBATED WITH A RESERVOIR SOLUTION ENRICHED BY 10 MM H2O2 AND 20% GLYCEROL TO GENERATE THE PEROXIDE
Crystal Properties
Matthews coefficientSolvent content
2.957.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.93α = 90
b = 95.08β = 90
c = 104.06γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MMIRRORS2013-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.35099.60.19.86.696758-1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3398.60.622.46.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUTNONE1.339.9791916484199.480.108830.107630.130.131550.15RANDOM13.027
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]
0.79-0.35-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free37.91
r_sphericity_bonded8.716
r_rigid_bond_restr1.823
r_scbond_it1.599
r_angle_refined_deg1.447
r_mcangle_it1.377
r_mcbond_other1.11
r_mcbond_it1.085
r_angle_other_deg0.77
r_chiral_restr0.086
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2360
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling