3PKH

Urate oxidase under 1.5 MPa / 15 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 Urate oxidase, 2 mg/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
2.9958.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.346α = 90
b = 96.337β = 90
c = 105.624γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 315rMIRRORS2010-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.9796ESRFBM30A

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
11.73099.40.03132.74.8443201
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)
11.711.898.80.15910.34.5

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 2IBA1.7119.4942111223899.60.168250.167030.19143RANDOM19.363
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.569
r_dihedral_angle_3_deg12.647
r_dihedral_angle_4_deg9.731
r_dihedral_angle_1_deg5.952
r_scangle_it4.246
r_scbond_it2.494
r_mcangle_it1.659
r_angle_refined_deg1.484
r_mcbond_it0.866
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.569
r_dihedral_angle_3_deg12.647
r_dihedral_angle_4_deg9.731
r_dihedral_angle_1_deg5.952
r_scangle_it4.246
r_scbond_it2.494
r_mcangle_it1.659
r_angle_refined_deg1.484
r_mcbond_it0.866
r_chiral_restr0.097
r_bond_refined_d0.012
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 Atoms188
Heterogen Atoms14

Software

Software
Software NamePurpose
ADSCdata collection
REFMACrefinement
XDSdata reduction
SCALAdata scaling