6S0W

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and kanamycin B sulfate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6S0T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52891:1 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 coefficientSolvent content
5.377.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.444α = 90
b = 186.061β = 95.2
c = 110.168γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210rRosenbaum-Rock vertical focusing mirro2017-06-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97915APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3544.2295.110.0780.73411.36.575259
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.390.821

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6S0T2.3644.2275259394695.110.187350.185380.22465RANDOM63.172
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]
-1.060.010.041
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.679
r_dihedral_angle_4_deg20.668
r_dihedral_angle_3_deg13.012
r_dihedral_angle_1_deg7.425
r_long_range_B_refined6.651
r_long_range_B_other6.587
r_mcangle_it2.55
r_mcangle_other2.55
r_scangle_other2.455
r_scbond_it1.522
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.679
r_dihedral_angle_4_deg20.668
r_dihedral_angle_3_deg13.012
r_dihedral_angle_1_deg7.425
r_long_range_B_refined6.651
r_long_range_B_other6.587
r_mcangle_it2.55
r_mcangle_other2.55
r_scangle_other2.455
r_scbond_it1.522
r_scbond_other1.522
r_mcbond_it1.473
r_mcbond_other1.473
r_angle_other_deg1.421
r_angle_refined_deg1.387
r_chiral_restr0.067
r_gen_planes_other0.018
r_gen_planes_refined0.01
r_bond_refined_d0.008
r_bond_other_d0.005
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 AtomsNumber
Protein Atoms13019
Nucleic Acid Atoms
Solvent Atoms1007
Heterogen Atoms306

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing