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The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, neamine and 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 0.02 M neamine
Crystal Properties Matthews coefficient Solvent content 5.36 77.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.467 α = 90 b = 185.25 β = 94.68 c = 110.46 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 EIGER X 9M Bimorph K-B pair 2018-07-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97938 APS 21-ID-D
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 3 48.54 90.74 0.126 0.982 6.6 5.2 40424
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 0.947 0.661
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 3 48.54 34821 1793 90.74 0.20112 0.19973 0.1973 0.22824 0.2264 RANDOM 60.168
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] 1.46 -0.36 0.22 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.501 r_dihedral_angle_4_deg 16.412 r_dihedral_angle_3_deg 13.403 r_long_range_B_other 9.526 r_long_range_B_refined 9.524 r_dihedral_angle_1_deg 7.568 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scangle_other 2.752 r_scbond_it 1.734
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.501 r_dihedral_angle_4_deg 16.412 r_dihedral_angle_3_deg 13.403 r_long_range_B_other 9.526 r_long_range_B_refined 9.524 r_dihedral_angle_1_deg 7.568 r_mcangle_it 2.794 r_mcangle_other 2.794 r_scangle_other 2.752 r_scbond_it 1.734 r_scbond_other 1.734 r_mcbond_it 1.584 r_mcbond_other 1.584 r_angle_refined_deg 1.351 r_angle_other_deg 1.337 r_chiral_restr 0.058 r_gen_planes_other 0.017 r_gen_planes_refined 0.009 r_bond_refined_d 0.007 r_bond_other_d 0.004 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 13104 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing