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Structure of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase (QDO)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 277 4.1-4.6M Sodium Formate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.23 61.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.138 α = 90 b = 90.138 β = 90 c = 168.735 γ = 120
Symmetry Space Group P 61 2 2
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 beamline optics 2006-01-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97929 APS 19-ID
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 2.6 50 96.8 0.055 5.1 23300 22906 69.3
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 2.6 2.7 83.4 0.168 4.2 1975
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 2.6 20 -1 11976 11976 617 96.35 0.23899 0.23692 0.23692 0.2411 0.27909 0.2979 RANDOM 73.343
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] 3.64 1.82 3.64 -5.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.853 r_dihedral_angle_3_deg 21.087 r_dihedral_angle_4_deg 21.044 r_dihedral_angle_1_deg 7.355 r_scangle_it 2.892 r_scbond_it 1.866 r_angle_refined_deg 1.731 r_mcangle_it 1.191 r_mcbond_it 0.811 r_symmetry_hbond_refined 0.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.853 r_dihedral_angle_3_deg 21.087 r_dihedral_angle_4_deg 21.044 r_dihedral_angle_1_deg 7.355 r_scangle_it 2.892 r_scbond_it 1.866 r_angle_refined_deg 1.731 r_mcangle_it 1.191 r_mcbond_it 0.811 r_symmetry_hbond_refined 0.333 r_nbtor_refined 0.327 r_nbd_refined 0.259 r_symmetry_vdw_refined 0.226 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.11 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2138 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling