5CQW

Tetragonal Complex Structure of Protein Kinase CK2 Catalytic Subunit with a Benzotriazole-Based Inhibitor Generated by click-chemistry


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NGA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP298Protein solution: 6 mg/ml CK2alpha, 1 mM Inhibitor, 10 %(v/v) DMSO, 250 mM NaCl, 12.5 mM Tris/HCl, pH 8.5; Reservoir: 25 %(w/v) PEG 3350, 0.2 M Lithiumsulfate, 0.1 M Bis-Tris/HCl, pH 5.5; drop: 1 Mikroliter pre-incubated CK2alpha/Inhibitor solution and 1 Mikroliter reservoir
Crystal Properties
Matthews coefficientSolvent content
3.261.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.092α = 90
b = 127.092β = 90
c = 126.836γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2012-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.0000SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.6544.931000.140.1413.17.430832
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.791001.1731.17324.5

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-VALUE3NGA2.6544.9341.3830757154799.920.18470.18240.2287Random
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_d12.261
f_angle_d0.584
f_chiral_restr0.025
f_bond_d0.002
f_plane_restr0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5586
Nucleic Acid Atoms
Solvent Atoms154
Heterogen Atoms131

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing