6SPW

Structure of protein kinase CK2 catalytic subunit with the CK2beta-competitive bisubstrate inhibitor ARC3140


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PVR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.151 MIKROLITER OF THE CK2ALPHA/ARC3140 MIXTURE (COMPOSITION: 7 MG/ML CK2ALPHA ENZYME, 1 MILLIMOLAR ARC3140, 10 % DIMETHYL SULFOXIDE, 450 MM NACL, 22.5 MM TRIS/HCL, PH 8.5) WAS MIXED WITH 2.5 MIKROLITER RESERVOIR SOLUTION (COMPOSITION: 30 % PEG4000, 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, PH 5.6) FOLLOWED BY VAPOUR DIFFUSION EQUILIBRATION AGAINST MICROLITER OF THE RESERVOIR SOLUTION.
Crystal Properties
Matthews coefficientSolvent content
2.0239.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.503α = 90
b = 85.171β = 90
c = 90.432γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.12713ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.59942.5999.80.10040.10040.99911.566.14916616.41
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.5991.65698.840.79380.79380.8941.986.1

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-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2PVR1.59942.5861.3549163196099.810.16580.16450.196
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_d12.145
f_angle_d1.377
f_chiral_restr0.098
f_bond_d0.017
f_plane_restr0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3005
Nucleic Acid Atoms
Solvent Atoms293
Heterogen Atoms1

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing