6RCG

Crystal structure of Casein kinase 1 delta (CK1 delta) complexed with SR3029 inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HNF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1520% PEG3350, 0.1M succinic acid
Crystal Properties
Matthews coefficientSolvent content
2.2745.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.04α = 90
b = 53.55β = 113.45
c = 72.17γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2013-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9200DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim 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
11.466.20996.70.0510.060.0310.998123.658592
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4897.50.4620.4620.5460.2860.872.43.5

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 REPLACEMENTTHROUGHOUT4HNF1.429.6355619297296.430.14420.14190.1854RANDOM23.78
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]
0.33-0.31-1.130.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.254
r_dihedral_angle_3_deg13.003
r_sphericity_bonded12.768
r_dihedral_angle_4_deg12.279
r_rigid_bond_restr8.718
r_dihedral_angle_1_deg6.161
r_angle_refined_deg1.656
r_angle_other_deg0.852
r_chiral_restr0.106
r_bond_refined_d0.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.254
r_dihedral_angle_3_deg13.003
r_sphericity_bonded12.768
r_dihedral_angle_4_deg12.279
r_rigid_bond_restr8.718
r_dihedral_angle_1_deg6.161
r_angle_refined_deg1.656
r_angle_other_deg0.852
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2409
Nucleic Acid Atoms
Solvent Atoms381
Heterogen Atoms78

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHASERphasing