5ZN0

Joint X-ray/neutron structure of protein kinase ck2 alpha subunit


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.52930.1M Tris-HCl, 0.85M ammonium sulfate, 5% acetonitrile, 2mM DTT
Crystal Properties
Matthews coefficientSolvent content
238.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.604α = 90
b = 45.442β = 111.83
c = 63.612γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152014-02-04MSINGLE WAVELENGTH
21neutron100IMAGE PLATEBIODIFF2014-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
2NUCLEAR REACTORFRM II BEAMLINE BIODIFF2.668FRM IIBIODIFF
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.13699.90.03821.35126644
21.933.8970.0918.5224039
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.11.140.3994.33.4
21.91.970.4511.61.6

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENT1.136.011.34126605633299.60.1880.1860.21232.7164
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT1.933.7624029120396.90.1910.1880.247
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.356
f_angle_d1.088
f_chiral_restr0.092
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2764
Nucleic Acid Atoms
Solvent Atoms418
Heterogen Atoms10

Software

Software
Software NamePurpose
PHENIXrefinement
PHASERphasing
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling