4QM7

Structure of bacterial polynucleotide kinase bound to GTP and pDNA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5293100 mM sodium citrate, 100 mM magnesium chloride, 18-24% PEG 6000, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2845.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.17α = 90
b = 67.21β = 90
c = 118.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130PIXELDECTRIS PILATUS 6M2013-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X251.1NSLSX25

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.823.199.7350743496999993
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8499.4

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONmolecular refinement1.823.0851.343493934905270799.530.16490.16280.1882random
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d20.654
f_angle_d1.526
f_chiral_restr0.104
f_bond_d0.014
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2722
Nucleic Acid Atoms63
Solvent Atoms357
Heterogen Atoms66

Software

Software
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing