8UWN

Crystal structure of human CLK1 kinase in complex with compound 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z57 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.83010.10 M Li2-Sulfate, 0.10 M Tris/HCl, pH 8.8, 15.00 %(w/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.752α = 90
b = 64.358β = 119.43
c = 80.822γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray101PIXELDECTRIS PILATUS3 2M2015-11-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.966ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (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
11.829.3597.90.1110.32.737677
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.997.40.622.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.829.3535813186497.780.180150.177090.24034RANDOM28.899
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]
0.54-0.441.12-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.429
r_dihedral_angle_4_deg17.201
r_dihedral_angle_3_deg14.404
r_long_range_B_refined9.869
r_long_range_B_other8.87
r_dihedral_angle_1_deg5.957
r_scangle_other5.359
r_mcangle_it3.867
r_mcangle_other3.867
r_scbond_it3.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.429
r_dihedral_angle_4_deg17.201
r_dihedral_angle_3_deg14.404
r_long_range_B_refined9.869
r_long_range_B_other8.87
r_dihedral_angle_1_deg5.957
r_scangle_other5.359
r_mcangle_it3.867
r_mcangle_other3.867
r_scbond_it3.536
r_scbond_other3.535
r_mcbond_it2.674
r_mcbond_other2.673
r_angle_refined_deg1.435
r_angle_other_deg0.963
r_chiral_restr0.087
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2762
Nucleic Acid Atoms
Solvent Atoms668
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing