3B1N

Structure of Burkholderia thailandensis nucleoside kinase (BthNK) in complex with ADP-mizoribine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.1	293	0.1M Na citrate, 13% PEG 3350, pH 5.1, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.583	α = 90
b = 164.654	β = 90
c = 182.54	γ = 90

Symmetry
Space Group	C 2 2 21

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	ADSC QUANTUM 315		2010-03-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.0000	Photon Factory	BL-5A

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	1.55	50	99.9	0.072	25.9	7		97659			12.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	100		0.438	5.9	6.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	SAD	THROUGHOUT	1.55	31.31	92736	4856	99.89	0.16809	0.16652	0.19826	RANDOM	17.722

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]
-0.29			-0.44		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.695
r_dihedral_angle_4_deg	17.242
r_dihedral_angle_3_deg	14.838
r_dihedral_angle_1_deg	5.964
r_scangle_it	4.747
r_scbond_it	2.976
r_mcangle_it	1.941
r_angle_refined_deg	1.901
r_mcbond_it	1.122
r_chiral_restr	0.126

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.695
r_dihedral_angle_4_deg	17.242
r_dihedral_angle_3_deg	14.838
r_dihedral_angle_1_deg	5.964
r_scangle_it	4.747
r_scbond_it	2.976
r_mcangle_it	1.941
r_angle_refined_deg	1.901
r_mcbond_it	1.122
r_chiral_restr	0.126
r_bond_refined_d	0.018
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4833
Nucleic Acid Atoms
Solvent Atoms	705
Heterogen Atoms	98

Software

Software
Software Name	Purpose
ADSC	data collection
SHELX	model building
SOLVE	phasing
RESOLVE	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
RESOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.