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Crystal structure of kynurenine aminotransferase II complex with alpha-ketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R2N PDB ENTRY 2R2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 100mM HEPES, 15% PEG 10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.93 α = 89.97 b = 72.09 β = 100.65 c = 109.079 γ = 93.88
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 2007-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.08090 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 2.5 29.69 0.106 89.6 3.4 63835
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 2.5 2.59 59.7 0.295 15.7 2.7
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 2R2N 2.5 29.69 54268 2890 88.72 0.21681 0.21537 0.2153 0.24412 0.242 RANDOM 33.861
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 40.794 r_dihedral_angle_3_deg 20.368 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_1_deg 9.279 r_scangle_it 3.965 r_scbond_it 2.757 r_angle_refined_deg 1.857 r_mcangle_it 1.73 r_mcbond_it 0.983 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.794 r_dihedral_angle_3_deg 20.368 r_dihedral_angle_4_deg 18.221 r_dihedral_angle_1_deg 9.279 r_scangle_it 3.965 r_scbond_it 2.757 r_angle_refined_deg 1.857 r_mcangle_it 1.73 r_mcbond_it 0.983 r_nbtor_refined 0.325 r_symmetry_hbond_refined 0.317 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.259 r_xyhbond_nbd_refined 0.213 r_chiral_restr 0.13 r_bond_refined_d 0.02 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13193 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASES phasing