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1.88 Angstrom Resolution Crystal Structure of Quercetin 2,3-dioxygenase from Acinetobacter baumannii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 292 8.5 mg/mL protein in 0.01 M Tris, pH 8.3, screen: Classics II (H1) (0.2 M ammonium acetate, 0.1 M Bis-Tris, pH 8.5, 25% w/v PEG3350)
Crystal Properties Matthews coefficient Solvent content 2.86 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.481 α = 90 b = 131.977 β = 103.58 c = 123.987 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 RAYONIX MX-300 C(111) 2018-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.88 30 99.9 0.094 0.094 0.107 0.05 15.7 4.5 120737 -3 24.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.88 1.91 100 0.763 0.763 0.865 0.404 0.649 2.1 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.88 29.81 114778 5945 99.8 0.15975 0.15821 0.1714 0.19039 0.1996 RANDOM 27.715
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 -0.41 0.33 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.251 r_sphericity_bonded 31.152 r_sphericity_free 21.502 r_dihedral_angle_4_deg 10.707 r_dihedral_angle_3_deg 9.89 r_long_range_B_refined 6.436 r_long_range_B_other 6.285 r_dihedral_angle_1_deg 4.323 r_scangle_other 3.772 r_scbond_it 2.428
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.251 r_sphericity_bonded 31.152 r_sphericity_free 21.502 r_dihedral_angle_4_deg 10.707 r_dihedral_angle_3_deg 9.89 r_long_range_B_refined 6.436 r_long_range_B_other 6.285 r_dihedral_angle_1_deg 4.323 r_scangle_other 3.772 r_scbond_it 2.428 r_scbond_other 2.428 r_mcangle_it 2.081 r_mcangle_other 2.081 r_mcbond_it 1.384 r_mcbond_other 1.383 r_angle_refined_deg 1.34 r_angle_other_deg 0.432 r_chiral_restr 0.058 r_gen_planes_refined 0.02 r_gen_planes_other 0.017 r_bond_refined_d 0.008 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8912 Nucleic Acid Atoms Solvent Atoms 1056 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing