3PJK

Urate oxidase under 1.0 MPa / 10 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, 8-AZAXANTHINE 0.2 MG/ML, TRIS 50 MM, PEG 8000 5-8%, NACL 0-50 MM, pH 8.5, BATCH, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.9758.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.117α = 90
b = 96.183β = 90
c = 105.463γ = 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
11.75097.10.04531.84.94376218.5
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)
11.71.7684.40.2963.53.7

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 2IBA1.70119.4541529220497.130.168010.166780.19171RANDOM20.711
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_3_deg11.862
r_dihedral_angle_4_deg9.612
r_dihedral_angle_1_deg6.035
r_scangle_it4.342
r_scbond_it2.525
r_mcangle_it1.704
r_angle_refined_deg1.481
r_mcbond_it0.89
r_chiral_restr0.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.154
r_dihedral_angle_3_deg11.862
r_dihedral_angle_4_deg9.612
r_dihedral_angle_1_deg6.035
r_scangle_it4.342
r_scbond_it2.525
r_mcangle_it1.704
r_angle_refined_deg1.481
r_mcbond_it0.89
r_chiral_restr0.097
r_bond_refined_d0.012
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2362
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms15

Software

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