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The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, ribostamycin B and 2-oxoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S0T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 1:1 of 28% PEG4000 (w/v), 0.2 M a-ketoglutaric acid disodium salt dihydrate, 0.1 M HEPES, and
15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl
Crystal Properties Matthews coefficient Solvent content 5.29 76.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.083 α = 90 b = 184.582 β = 94.97 c = 110.333 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 100 PIXEL DECTRIS PILATUS3 6M Rosenbaum-Rock vertical focusing mirror 2017-06-30 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97930 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.4 47.27 91.12 0.098 0.993 7.3 6.9 67239 -3 36.1
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 2.54 0.863
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 FOURIER SYNTHESIS THROUGHOUT 6S0T 2.4 47.27 67239 3576 91.12 0.17437 0.17276 0.1767 0.2042 0.2035 RANDOM 50.681
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] -0.95 0.67 0.34 0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_4_deg 20.302 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 7.148 r_long_range_B_refined 6.261 r_long_range_B_other 6.253 r_scangle_other 4.272 r_mcangle_other 3.129 r_mcangle_it 3.122 r_scbond_it 2.927
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.342 r_dihedral_angle_4_deg 20.302 r_dihedral_angle_3_deg 13.44 r_dihedral_angle_1_deg 7.148 r_long_range_B_refined 6.261 r_long_range_B_other 6.253 r_scangle_other 4.272 r_mcangle_other 3.129 r_mcangle_it 3.122 r_scbond_it 2.927 r_scbond_other 2.927 r_mcbond_it 2.017 r_mcbond_other 1.986 r_angle_refined_deg 1.455 r_angle_other_deg 1.261 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13030 Nucleic Acid Atoms Solvent Atoms 462 Heterogen Atoms 255
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing