3E9K

Crystal structure of Homo sapiens kynureninase-3-hydroxyhippuric acid inhibitor complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HZPPDB entry 2HZP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH UNDER OIL5.12298HKynase solution (9 mg/mL in 50 mM HEPES pH 5.1, and 0.1 mM PLP) mixed (1:1 ratio) with a crystallization solution containing 0.05 M MgCl2, 0.1 M Tris-HCl pH 8.0, 25% PEG 3000, 350 mM HHA, pH 5.12, MICROBATCH UNDER OIL, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.444α = 90
b = 77.124β = 109.35
c = 94.558γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes2007-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID1.007APS19-ID

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
11.789.0998.550.052519065190616.68
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)
11.71.74486.660.039

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 REPLACEMENTTHROUGHOUTPDB entry 2HZP1.789.0951906280298.550.155120.15320.19133RANDOM16.686
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]
-0.44-0.87-0.250.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.278
r_dihedral_angle_4_deg19.569
r_dihedral_angle_3_deg11.999
r_dihedral_angle_1_deg5.373
r_scangle_it4.351
r_scbond_it2.973
r_mcangle_it1.65
r_angle_refined_deg1.065
r_mcbond_it0.894
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.278
r_dihedral_angle_4_deg19.569
r_dihedral_angle_3_deg11.999
r_dihedral_angle_1_deg5.373
r_scangle_it4.351
r_scbond_it2.973
r_mcangle_it1.65
r_angle_refined_deg1.065
r_mcbond_it0.894
r_nbtor_refined0.306
r_nbd_refined0.196
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.095
r_symmetry_hbond_refined0.088
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.004
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_refined
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 Atoms3547
Nucleic Acid Atoms
Solvent Atoms632
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing