3B1N

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.12930.1M Na citrate, 13% PEG 3350, pH 5.1, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.583α = 90
b = 164.654β = 90
c = 182.54γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.555099.90.07225.979765912.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.581000.4385.96.8

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 DIFFRACTIONSADTHROUGHOUT1.5531.3192736485699.890.168090.166520.19826RANDOM17.722
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]
-0.29-0.440.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.695
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg14.838
r_dihedral_angle_1_deg5.964
r_scangle_it4.747
r_scbond_it2.976
r_mcangle_it1.941
r_angle_refined_deg1.901
r_mcbond_it1.122
r_chiral_restr0.126
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.695
r_dihedral_angle_4_deg17.242
r_dihedral_angle_3_deg14.838
r_dihedral_angle_1_deg5.964
r_scangle_it4.747
r_scbond_it2.976
r_mcangle_it1.941
r_angle_refined_deg1.901
r_mcbond_it1.122
r_chiral_restr0.126
r_bond_refined_d0.018
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4833
Nucleic Acid Atoms
Solvent Atoms705
Heterogen Atoms98

Software

Software
Software NamePurpose
ADSCdata collection
SHELXmodel building
SOLVEphasing
RESOLVEmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing