6S0U

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel and 2-oxoglutarate


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52891:1 of 25% PEG4000, 0.2 M alpha-Ketoglutaric acid disodium salt dihydrate, 0.05 M bis-tris methane, 0.15 M NaCl and 15mg/ml protein in 0.05 M bis-tris methane, 0.15 M NaCl
Crystal Properties
Matthews coefficientSolvent content
5.2176.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.825α = 90
b = 183.691β = 96.55
c = 110.169γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MRosenbaum-Rock vertical focusing mirror2017-06-30MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97930APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.1445.7392.20.1796.23.910504526.1
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)RedundancyNumber Unique Reflections (All)
12.152.190.690.579

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 SYNTHESISTHROUGHOUT6S0T2.1545.7393360483992.190.19820.195810.24429RANDOM33.238
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]
-0.410.47-1.21.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.703
r_dihedral_angle_4_deg15.155
r_dihedral_angle_3_deg13.079
r_dihedral_angle_1_deg7.29
r_long_range_B_refined6.562
r_long_range_B_other6.562
r_scangle_other3.545
r_mcangle_it2.59
r_mcangle_other2.59
r_scbond_other2.393
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.703
r_dihedral_angle_4_deg15.155
r_dihedral_angle_3_deg13.079
r_dihedral_angle_1_deg7.29
r_long_range_B_refined6.562
r_long_range_B_other6.562
r_scangle_other3.545
r_mcangle_it2.59
r_mcangle_other2.59
r_scbond_other2.393
r_scbond_it2.392
r_mcbond_it1.685
r_mcbond_other1.685
r_angle_refined_deg1.54
r_angle_other_deg1.341
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms12906
Nucleic Acid Atoms
Solvent Atoms1161
Heterogen Atoms83

Software

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