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Crystal Structure of Human Kynurenine Aminotransferase I in Complex with Indole-3-acetic Acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W7L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 22% PEG 400, sodium acetate 0.2 M, Tris 0.1 M, 4% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.24 44.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.364 α = 90 b = 108.454 β = 114.2 c = 81.867 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 ADSC QUANTUM 315 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 30 0.049 7.3 122095
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 0.52 3.8 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1W7L 1.55 29.22 115737 6120 99.76 0.18581 0.18451 0.21014 0.2084 RANDOM 20.974
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] 0.03 0.01 0.03 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.737 r_dihedral_angle_4_deg 16.407 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 8.398 r_scangle_it 3.097 r_scbond_it 1.967 r_angle_refined_deg 1.33 r_mcangle_it 1.259 r_mcbond_it 0.697 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.737 r_dihedral_angle_4_deg 16.407 r_dihedral_angle_3_deg 12.887 r_dihedral_angle_1_deg 8.398 r_scangle_it 3.097 r_scbond_it 1.967 r_angle_refined_deg 1.33 r_mcangle_it 1.259 r_mcbond_it 0.697 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.199 r_metal_ion_refined 0.149 r_symmetry_hbond_refined 0.12 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 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_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 6738 Nucleic Acid Atoms Solvent Atoms 590 Heterogen Atoms 58
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling