3OFM

Structure of a human CK2alpha prime, the paralog isoform of the catalytic subunit of protein kinase CK2 from Homo sapiens


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Protein stock solution: 6 mg/ml protein, 25 mM Tris/HCl, pH 8.5, 500 mM sodium chloride, 1 mM inhibitor 3-(4,5,6,7-tetrabromo-1H-benzotriazol-1-yl)propan-1-ol Reservoir: 28 % PEG6000, 500 mM lithium chloride, 100 mM Tris/HCl, pH 8.5 Drop: mixture of 0.5 uL protein solution plus 0.5 uL reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.69α = 112.4
b = 47.57β = 89.49
c = 50.57γ = 91.3
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
1233.0386.80.0570.05712.612.22726523663-326.083
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)
122.0547.70.2573.4

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2PVR233.032726522479118486.80.173780.171970.20721RANDOM26.698
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]
1.01-0.20.34-0.26-1.11-1.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.102
r_dihedral_angle_4_deg14.052
r_dihedral_angle_3_deg11.425
r_dihedral_angle_1_deg5.1
r_scangle_it4.127
r_scbond_it2.89
r_mcangle_it2.208
r_mcbond_it1.46
r_angle_refined_deg0.975
r_angle_other_deg0.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.102
r_dihedral_angle_4_deg14.052
r_dihedral_angle_3_deg11.425
r_dihedral_angle_1_deg5.1
r_scangle_it4.127
r_scbond_it2.89
r_mcangle_it2.208
r_mcbond_it1.46
r_angle_refined_deg0.975
r_angle_other_deg0.776
r_mcbond_other0.591
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2749
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms18

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling