3R0T

Crystal structure of human protein kinase CK2 alpha subunit in complex with the inhibitor CX-5279


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529332% PEG 4000, 0.2M Li2SO4, 0.1M Tris pH 8.5, vapor diffusion, sitting drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9737.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.352α = 90
b = 46.184β = 111.51
c = 63.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMirrors2010-10-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1ELETTRA5.2R

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
11.7546.1889.60.08382.8285512855117.833
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)
11.751.8457.40.4620.4621.71.62619

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTpdb entry 2PVR1.7535.17728526142089.440.16280.16020.2107RANDOM24.0662
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]
-6.3098-1.16513.47992.8299
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.608
f_angle_d1.036
f_chiral_restr0.075
f_bond_d0.007
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2765
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms95

Software

Software
Software NamePurpose
SCALAdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
Elettradata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing