2IBA

Urate oxidase from Aspergillus flavus complexed with its inhibitor 8-azaxanthine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R51PDB ENTRY 1R51

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.529810MG/ML URATE OXIDASE, 8-AZAXANTHINE 0.2MG/ML, TRIS 20mM, PEG 8000 7%, NACL 200mM, batch, TEMPERATURE 298K, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.9858.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.492α = 90
b = 96.041β = 90
c = 105.343γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray277CCDMARRESEARCH2005-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.972ESRFBM14

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
11.55091.10.05610.85.465481596531118.06
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)
11.51.5587.90.2712.85710

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRIGID BODYTHROUGHOUTPDB ENTRY 1R511.514.8759516302190.990.1770.1760.197RANDOM20.872
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.722
r_dihedral_angle_3_deg12.491
r_dihedral_angle_4_deg8.661
r_dihedral_angle_1_deg5.908
r_scangle_it3.564
r_scbond_it2.165
r_mcangle_it1.5
r_angle_refined_deg1.408
r_mcbond_it0.788
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.722
r_dihedral_angle_3_deg12.491
r_dihedral_angle_4_deg8.661
r_dihedral_angle_1_deg5.908
r_scangle_it3.564
r_scbond_it2.165
r_mcangle_it1.5
r_angle_refined_deg1.408
r_mcbond_it0.788
r_nbtor_refined0.307
r_symmetry_vdw_refined0.206
r_nbd_refined0.201
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.094
r_chiral_restr0.088
r_metal_ion_refined0.066
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms12

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection