7Z6O

X-Ray studies of Ku70/80 reveal the binding site for IP6


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JEY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529324% PEG3350, 200mM Na2SO4, 100mM BTP, 5 mM b-mercaptoethanol
Crystal Properties
Matthews coefficientSolvent content
4.2671.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.146α = 90
b = 125.146β = 90
c = 319.7γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2020-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.980101SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
13.748.399.70.9964.220.131855115.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.73.7998.40.04718.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1jey3.748.31.351277865540.070.22050.21790.2713RANDOM209.23
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_d15.5248
f_angle_d0.4224
f_chiral_restr0.0375
f_plane_restr0.003
f_bond_d0.0016
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8326
Nucleic Acid Atoms571
Solvent Atoms
Heterogen Atoms36

Software

Software
Software NamePurpose
BUSTERrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
STARANISOdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
MxCuBEdata collection
Cootmodel building