3FWQ

Inactive conformation of human protein kinase CK2 catalytic subunit


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein stock solution: 10mg/ml CK2alpha, 500mM sodium chloride, 25mM Tris/HCl, pH 8.5; Reservoir: 2M ammonium sulfate, 2M sodium chloride; Drop: 0.001mL reservoir solution, 0.001mL protein stock solution, 0.003mL 1mM AMPPNP, 0.0006mL 10mM magnesium chloride, 0.0001mL glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9938.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.324α = 90
b = 71.324β = 90
c = 125.681γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2007-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X120.95370EMBL/DESY, HAMBURGX12

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
12.334.596.90.10.117.67.7278632699947.1
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)
12.32.3898.30.72427.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2PVR2.334.32704625746125396.90.172560.172560.169690.23272RANDOM41.145
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]
7.877.87-15.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.377
r_dihedral_angle_4_deg15.562
r_dihedral_angle_3_deg15.173
r_dihedral_angle_1_deg4.734
r_mcangle_it2.556
r_scangle_it2.175
r_mcbond_it1.612
r_scbond_it1.558
r_angle_refined_deg0.885
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.377
r_dihedral_angle_4_deg15.562
r_dihedral_angle_3_deg15.173
r_dihedral_angle_1_deg4.734
r_mcangle_it2.556
r_scangle_it2.175
r_mcbond_it1.612
r_scbond_it1.558
r_angle_refined_deg0.885
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5634
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms28

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling