3PKU

Urate oxidase under 1 MPa / 10 bars pressure of nitrous oxide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IBAPDB entry 2IBA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH8.529810-15 mg/ml urate oxidase, 2mg/ml 8-azaxanthine, 50 mM Tris/HCl pH 8.5, 5-8 % PEG 8000, 0-0.05 M NaCl, BATCH, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9758.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.12α = 90
b = 96.211β = 90
c = 105.456γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATEMAR scanner 345 mm plateMirrors2007-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.753099.10.044344.9410221
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8191.70.25.54.53756

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 2IBA1.7514.9738884206099.090.164990.163430.19562RANDOM20.808
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_deg38.824
r_dihedral_angle_3_deg12.393
r_dihedral_angle_4_deg10.212
r_dihedral_angle_1_deg5.955
r_scangle_it4.359
r_scbond_it2.643
r_mcangle_it1.723
r_angle_refined_deg1.44
r_mcbond_it0.901
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.824
r_dihedral_angle_3_deg12.393
r_dihedral_angle_4_deg10.212
r_dihedral_angle_1_deg5.955
r_scangle_it4.359
r_scbond_it2.643
r_mcangle_it1.723
r_angle_refined_deg1.44
r_mcbond_it0.901
r_nbtor_refined0.309
r_nbd_refined0.208
r_symmetry_vdw_refined0.171
r_symmetry_hbond_refined0.123
r_xyhbond_nbd_refined0.119
r_chiral_restr0.105
r_metal_ion_refined0.037
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms16

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling