6S0T

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S0R

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 0.1 M potassium iodide

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.614	α = 90
b = 186.468	β = 95.74
c = 110.828	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	CCD	MARMOSAIC 300 mm CCD	beryllium lens	2017-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	2.1	50	96.42	0.063	0.754	9.6	3.8		118025		-3	29.7

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	2.1	2.14	100		0.666	0.829	2.1	3.8

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6S0R	2.1	50	108651	5621	96.42	0.17091	0.1692	0.20424	RANDOM	35.984

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]
-0.34		0.48	0.09		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.777
r_dihedral_angle_4_deg	22.016
r_sphericity_bonded	15.532
r_dihedral_angle_3_deg	12.268
r_long_range_B_refined	7.072
r_long_range_B_other	6.921
r_dihedral_angle_1_deg	6.268
r_scangle_other	2.547
r_mcangle_it	2.217
r_mcangle_other	2.217
r_scbond_it	1.91
r_scbond_other	1.653
r_angle_refined_deg	1.515
r_mcbond_it	1.352
r_mcbond_other	1.352
r_angle_other_deg	0.97
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12937
Nucleic Acid Atoms
Solvent Atoms	1627
Heterogen Atoms	123

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing