4EK2

The structure of nucleoside diphosphate kinase (NDK) from Burkholderia thailandensis bound to deoxyadenosine monophosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DUTPDB ENTRY 4DUT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7289ButhA.00438.a.A1 PS01186 at 42.64 mg/mL in 1.5 M ammonium sulfate, 0.1 M Bis-Tris propane, pH 7.0, 10 mM dAMP, cryoprotectant: 15% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.9257.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.68α = 90
b = 90.68β = 90
c = 90.43γ = 90
Symmetry
Space GroupP 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442012-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
1240.55397.20.06630.2125415-319.831
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)
122.0584.40.2197.95

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4DUT240.55325383129597.220.19160.18970.2282RANDOM16.6122
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]
-0.24-0.240.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg18.641
r_dihedral_angle_3_deg14.022
r_dihedral_angle_1_deg5.729
r_scangle_it3.149
r_scbond_it1.885
r_angle_refined_deg1.332
r_mcangle_it1.103
r_angle_other_deg0.923
r_mcbond_it0.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.722
r_dihedral_angle_4_deg18.641
r_dihedral_angle_3_deg14.022
r_dihedral_angle_1_deg5.729
r_scangle_it3.149
r_scbond_it1.885
r_angle_refined_deg1.332
r_mcangle_it1.103
r_angle_other_deg0.923
r_mcbond_it0.615
r_mcbond_other0.159
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2162
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms36

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction