7PUF

urate oxidase azaxanthine complex under 600 bar (60 MPa) of argon


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R51dimer reconstructed from pdbid 1R51

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE829820 microLiter (17 mg/mL protein, BUFFER Tris/Acetate pH 8) mixed with 20 microLiter PEG 4000 8% (same pH)
Crystal Properties
Matthews coefficientSolvent content
2.9157.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.225α = 90
b = 95.268β = 90
c = 104.5γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B1.7712ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.8647.781.50.0630.0670.0260.99921.411.35384212.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.861.920.10.1820.2220.1510.952.83.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTdimer reconstructed from pdbid 1R511.8647.6851064272681.20.1640.1620.228RANDOM17.38
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.183
r_dihedral_angle_4_deg18.06
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg7.938
r_angle_other_deg1.303
r_angle_refined_deg1.297
r_chiral_restr0.059
r_gen_planes_refined0.009
r_bond_refined_d0.007
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.183
r_dihedral_angle_4_deg18.06
r_dihedral_angle_3_deg15.125
r_dihedral_angle_1_deg7.938
r_angle_other_deg1.303
r_angle_refined_deg1.297
r_chiral_restr0.059
r_gen_planes_refined0.009
r_bond_refined_d0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4724
Nucleic Acid Atoms
Solvent Atoms546
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing