6TLP

HUMAN CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52900.1 M sodium HEPES/MOPS buffer pH 7.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM sodium citrate tribasic dihydrate, 20 mM sodium potassium tartrate tetrahydrate, 20 mM sodium oxamate, 20% polyethylene glycol 550 monomethyl ester, 10% polyethylene glycol 20000
Crystal Properties
Matthews coefficientSolvent content
2.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.224α = 90
b = 127.224β = 90
c = 60.881γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-11-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P110.91170PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)CC (Half)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
11.9336.1899.90.1390.1420.99922.6926.243822636.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.932.0499.51.6691.7030.8071.9825.37

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation 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 REPLACEMENTTHROUGHOUT3WAR1.9336.1836284194299.880.1550.15330.1886RANDOM35.503
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]
0.640.64-1.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.252
r_dihedral_angle_4_deg18.43
r_dihedral_angle_3_deg14.542
r_dihedral_angle_1_deg6.109
r_angle_refined_deg1.268
r_angle_other_deg1.238
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.252
r_dihedral_angle_4_deg18.43
r_dihedral_angle_3_deg14.542
r_dihedral_angle_1_deg6.109
r_angle_refined_deg1.268
r_angle_other_deg1.238
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2812
Nucleic Acid Atoms
Solvent Atoms529
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARP/wARPmodel building
PDB_EXTRACTdata extraction