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Crystal Structure of Homo Sapiens Kynureninase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZ9 PDB ENTRY 1QZ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch under oil 8 298 A 9.2 mg/ml kynureninase solution in 50 mM HEPES pH 5.2, 0.2 mM PLP was mixed in equal parts with 0.1 M Tris-Cl pH 8.0, 0.05 M MgCl2, 25% PEG 3000, Microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.117 α = 90 b = 76.838 β = 108.7 c = 93.274 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2004-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97934 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 88.39 99.8 0.055 0.055 24.68 3.7 33266 21.969
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.08 98.8 0.264 0.264 5.046 3.3 3279
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QZ9 2 88.39 31583 1683 99.46 0.15217 0.14986 0.1693 0.19534 0.1989 RANDOM, 5% 21.969
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] -0.68 -1.44 -0.32 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 19.397 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 7.418 r_scangle_it 4.688 r_scbond_it 3.183 r_mcangle_it 1.67 r_angle_refined_deg 1.135 r_mcbond_it 0.895 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.407 r_dihedral_angle_4_deg 19.397 r_dihedral_angle_3_deg 13.04 r_dihedral_angle_1_deg 7.418 r_scangle_it 4.688 r_scbond_it 3.183 r_mcangle_it 1.67 r_angle_refined_deg 1.135 r_mcbond_it 0.895 r_nbtor_refined 0.303 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.134 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 Atoms Number Protein Atoms 3556 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing