7K17

Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7K0Y 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000
2VAPOR DIFFUSION, HANGING DROP2930.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.8668.15
3.8668.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.12α = 90
b = 132.64β = 105.53
c = 296.59γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2012-05-23MSINGLE WAVELENGTH
22x-ray100PIXELDECTRIS PILATUS 6M-F2011-06-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9791ESRFID29
2SYNCHROTRONESRF BEAMLINE ID23-10.9791ESRFID23-1

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
14.349.91897.80.1615.435.286508185.23
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)
14.34.40750.936

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7K0Y4.349.9284525197897.80.2870.28590.3353217.04
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_d21.5967
f_angle_d0.8611
f_chiral_restr0.0461
f_plane_restr0.0054
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms56895
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
PHENIXphasing