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Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AOV PDB entry 3AOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 0.1M imidazole pH 8.0, 0.2M calcium acetate, 20% w/v PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.03 39.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.769 α = 90 b = 70.997 β = 90.02 c = 136.704 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 210 mirrors 2010-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
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 1.58 50 96.8 0.049 3.5 109166
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 1.58 1.64 99.3 0.545 2.07 3.4
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 3AOV 1.58 50 103708 5458 96.61 0.18288 0.18046 0.1831 0.22975 0.2297 RANDOM 25.781
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] -1.58 -0.18 1.51 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 15.127 r_dihedral_angle_1_deg 8.734 r_scangle_it 6.02 r_scbond_it 3.844 r_angle_refined_deg 2.503 r_mcangle_it 2.439 r_mcbond_it 1.461 r_chiral_restr 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.241 r_dihedral_angle_4_deg 21.744 r_dihedral_angle_3_deg 15.127 r_dihedral_angle_1_deg 8.734 r_scangle_it 6.02 r_scbond_it 3.844 r_angle_refined_deg 2.503 r_mcangle_it 2.439 r_mcbond_it 1.461 r_chiral_restr 0.174 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6494 Nucleic Acid Atoms Solvent Atoms 829 Heterogen Atoms 124
Software Software Software Name Purpose BL38B1 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling