5OWQ

Human STK10 bound to dovitinib


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherSTK10

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1M sodium formate, 15%(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.57α = 90
b = 50.4β = 96.6
c = 114.57γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2012-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.757.1991.40.140.9844.72.816619
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.8691.80.610.6921.32.7

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 REPLACEMENTTHROUGHOUTSTK102.757.191567483890.330.265350.263220.30495RANDOM54.895
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]
2.441.36-0.89-1.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.964
r_dihedral_angle_3_deg18.044
r_dihedral_angle_4_deg12.714
r_dihedral_angle_1_deg7.346
r_long_range_B_refined3.869
r_long_range_B_other3.869
r_angle_refined_deg1.693
r_scangle_other1.535
r_mcangle_it1.495
r_mcangle_other1.495
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.964
r_dihedral_angle_3_deg18.044
r_dihedral_angle_4_deg12.714
r_dihedral_angle_1_deg7.346
r_long_range_B_refined3.869
r_long_range_B_other3.869
r_angle_refined_deg1.693
r_scangle_other1.535
r_mcangle_it1.495
r_mcangle_other1.495
r_angle_other_deg1.06
r_scbond_other0.859
r_scbond_it0.858
r_mcbond_it0.817
r_mcbond_other0.817
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3843
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing