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The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus complex with nickel, sulfate and chloride
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
Crystal Properties Matthews coefficient Solvent content 5.3 76.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.368 α = 90 b = 184.213 β = 94.23 c = 110.148 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 2017-03-10 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.48484 APS 21-ID-D
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 2.5 50 87.54 0.102 6.7 5.8 123338 -3 37.7
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 2.5 2.54 0.977 0.451
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 FOURIER SYNTHESIS THROUGHOUT 2.5 47.22 57296 3043 87.54 0.17165 0.16972 0.177 0.20772 0.2147 RANDOM 47.372
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] -0.78 0.62 0.09 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.864 r_dihedral_angle_4_deg 19.279 r_dihedral_angle_3_deg 13.888 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 5.148 r_long_range_B_other 4.983 r_mcangle_it 2.213 r_mcangle_other 2.213 r_scangle_other 2.133 r_scbond_it 1.501
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.864 r_dihedral_angle_4_deg 19.279 r_dihedral_angle_3_deg 13.888 r_dihedral_angle_1_deg 7.379 r_long_range_B_refined 5.148 r_long_range_B_other 4.983 r_mcangle_it 2.213 r_mcangle_other 2.213 r_scangle_other 2.133 r_scbond_it 1.501 r_angle_refined_deg 1.426 r_scbond_other 1.318 r_mcbond_it 1.277 r_mcbond_other 1.272 r_angle_other_deg 1.23 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 13061 Nucleic Acid Atoms Solvent Atoms 757 Heterogen Atoms 112
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing