2PVR

Crystal structure of the catalytic subunit of protein kinase CK2 (C-terminal deletion mutant 1-335) in complex with two sulfate ions


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PJKPDB entry 1PJK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEGmme 5000, ammonium sulfate, MES, adenylyl imidodiphosphate, magnesium chloride, peptide RRRADDSDDDDD, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.9737.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.67α = 90
b = 45.371β = 111.22
c = 63.442γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic multilayer mirror2003-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.60519.7199.60.14210.54.7406264046421.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.6051.799.246.63.24.25999

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 1PJK1.60519.71406663863220341000.18680.18680.183960.24146RANDOM10.401
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]
0.2-0.330.19-0.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.153
r_dihedral_angle_4_deg18.45
r_dihedral_angle_3_deg13.497
r_scangle_it6.516
r_dihedral_angle_1_deg5.562
r_mcangle_it4.798
r_scbond_it4.712
r_mcbond_it4.195
r_angle_refined_deg1.223
r_mcbond_other1.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.153
r_dihedral_angle_4_deg18.45
r_dihedral_angle_3_deg13.497
r_scangle_it6.516
r_dihedral_angle_1_deg5.562
r_mcangle_it4.798
r_scbond_it4.712
r_mcbond_it4.195
r_angle_refined_deg1.223
r_mcbond_other1.103
r_angle_other_deg0.873
r_symmetry_vdw_other0.25
r_nbd_refined0.205
r_nbd_other0.187
r_nbtor_refined0.181
r_symmetry_vdw_refined0.181
r_symmetry_hbond_refined0.175
r_xyhbond_nbd_refined0.139
r_nbtor_other0.081
r_chiral_restr0.072
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms2771
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms41

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction