3PK4

Urate oxidase under 3.2 MPa / 32 bars pressure of xenon


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-1 Urate oxidase; 2 mg.ml-1 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
2.9958.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.405α = 90
b = 96.311β = 90
c = 105.593γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315rMIRRORS2010-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9797ESRFBM30A

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
11.853099.90.06415.34.8352881
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)
11.851.9599.999.90.315.14.8

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 2IBA1.8519.7633452176699.750.161090.159360.19341RANDOM25.571
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.126
r_dihedral_angle_3_deg12.715
r_dihedral_angle_4_deg11.375
r_dihedral_angle_1_deg6.038
r_scangle_it4.546
r_scbond_it2.675
r_mcangle_it1.786
r_angle_refined_deg1.546
r_mcbond_it0.928
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.126
r_dihedral_angle_3_deg12.715
r_dihedral_angle_4_deg11.375
r_dihedral_angle_1_deg6.038
r_scangle_it4.546
r_scbond_it2.675
r_mcangle_it1.786
r_angle_refined_deg1.546
r_mcbond_it0.928
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms163
Heterogen Atoms14

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling