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The crystal structure of human kynurenine aminotransferase II in complex with kynurenine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QLR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 100 mM Hepes, 15% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.843 α = 90 b = 109.36 β = 94.68 c = 119.354 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2007-06-27 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 1.95 30 93.2 0.092 11.5 132070
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 1.95 2.02 62.1 0.373 6.5
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 2qlr 1.95 26.68 116774 6185 93.14 0.19568 0.19425 0.1942 0.2228 0.2234 RANDOM 29.617
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.658 r_dihedral_angle_4_deg 18.484 r_dihedral_angle_3_deg 18.237 r_dihedral_angle_1_deg 7.676 r_scangle_it 4.3 r_scbond_it 2.827 r_angle_refined_deg 1.796 r_mcangle_it 1.71 r_mcbond_it 0.958 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.658 r_dihedral_angle_4_deg 18.484 r_dihedral_angle_3_deg 18.237 r_dihedral_angle_1_deg 7.676 r_scangle_it 4.3 r_scbond_it 2.827 r_angle_refined_deg 1.796 r_mcangle_it 1.71 r_mcbond_it 0.958 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.268 r_nbd_refined 0.231 r_chiral_restr 0.207 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.139 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13330 Nucleic Acid Atoms Solvent Atoms 1341 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing