6S0R

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


X-RAY DIFFRACTION

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
Crystal Properties
Matthews coefficientSolvent content
5.376.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.368α = 90
b = 184.213β = 94.23
c = 110.148γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9MBimorph K-B pair2017-03-10MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.48484APS21-ID-D

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
12.55087.540.1026.75.8123338-337.7
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)RedundancyNumber Unique Reflections (All)
12.52.540.9770.451

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 SYNTHESISTHROUGHOUT2.547.2257296304387.540.171650.169720.20772RANDOM47.372
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]
-0.780.620.090.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.864
r_dihedral_angle_4_deg19.279
r_dihedral_angle_3_deg13.888
r_dihedral_angle_1_deg7.379
r_long_range_B_refined5.148
r_long_range_B_other4.983
r_mcangle_it2.213
r_mcangle_other2.213
r_scangle_other2.133
r_scbond_it1.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.864
r_dihedral_angle_4_deg19.279
r_dihedral_angle_3_deg13.888
r_dihedral_angle_1_deg7.379
r_long_range_B_refined5.148
r_long_range_B_other4.983
r_mcangle_it2.213
r_mcangle_other2.213
r_scangle_other2.133
r_scbond_it1.501
r_angle_refined_deg1.426
r_scbond_other1.318
r_mcbond_it1.277
r_mcbond_other1.272
r_angle_other_deg1.23
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms13061
Nucleic Acid Atoms
Solvent Atoms757
Heterogen Atoms112

Software

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