6S0U | pdb_00006s0u

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6S0T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	1:1 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 coefficient	Solvent content
5.21	76.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.825	α = 90
b = 183.691	β = 96.55
c = 110.169	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 PILATUS3 6M	Rosenbaum-Rock vertical focusing mirror	2017-06-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97930	APS	19-ID

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	2.14	45.73	92.2	0.179	6.2	3.9		105045			26.1

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)	Redundancy	Number Unique Reflections (All)
1	2.15	2.19			0.69	0.579

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	6S0T	2.15	45.73	93360	4839	92.19	0.1982	0.19581	0.2	0.24429	0.25	RANDOM	33.238

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]
-0.41		0.47	-1.2		1.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.703
r_dihedral_angle_4_deg	15.155
r_dihedral_angle_3_deg	13.079
r_dihedral_angle_1_deg	7.29
r_long_range_B_refined	6.562
r_long_range_B_other	6.562
r_scangle_other	3.545
r_mcangle_it	2.59
r_mcangle_other	2.59
r_scbond_other	2.393
r_scbond_it	2.392
r_mcbond_it	1.685
r_mcbond_other	1.685
r_angle_refined_deg	1.54
r_angle_other_deg	1.341
r_chiral_restr	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	12906
Nucleic Acid Atoms
Solvent Atoms	1161
Heterogen Atoms	83

Software

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