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The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and kanamycin B sulfate
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, HANGING DROP 7.5 289 1:1 of 28% PEG4000 (w/v), 0.5 M lithium sulfate, 0.1 M HEPES, 0.1 M sodium acetate and
15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl; soaked with 0.05 M kanamycin B
Crystal Properties Matthews coefficient Solvent content 5.3 77.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.444 α = 90 b = 186.061 β = 95.2 c = 110.168 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 CCD ADSC QUANTUM 210r Rosenbaum-Rock vertical focusing mirro 2017-06-17 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97915 APS 19-BM
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 2.35 44.22 95.11 0.078 0.734 11.3 6.5 75259
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 2.35 2.39 0.821
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 2.36 44.22 75259 3946 95.11 0.18735 0.18538 0.1909 0.22465 0.2284 RANDOM 63.172
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] -1.06 0.01 0.04 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 7.425 r_long_range_B_refined 6.651 r_long_range_B_other 6.587 r_mcangle_it 2.55 r_mcangle_other 2.55 r_scangle_other 2.455 r_scbond_it 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.679 r_dihedral_angle_4_deg 20.668 r_dihedral_angle_3_deg 13.012 r_dihedral_angle_1_deg 7.425 r_long_range_B_refined 6.651 r_long_range_B_other 6.587 r_mcangle_it 2.55 r_mcangle_other 2.55 r_scangle_other 2.455 r_scbond_it 1.522 r_scbond_other 1.522 r_mcbond_it 1.473 r_mcbond_other 1.473 r_angle_other_deg 1.421 r_angle_refined_deg 1.387 r_chiral_restr 0.067 r_gen_planes_other 0.018 r_gen_planes_refined 0.01 r_bond_refined_d 0.008 r_bond_other_d 0.005 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 13019 Nucleic Acid Atoms Solvent Atoms 1007 Heterogen Atoms 306
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing