5OWT

Crystal structure of TNKS2 in complex with (5S)-5-methyl-5-[4-(4-oxo-3,4-dihydroquinazolin-2-yl)phenyl]imidazolidine-2,4-dione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U9H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52770.2 M LISO4, 0.1 M TRIS HCL, 22% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.2745.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89α = 90
b = 98.23β = 90
c = 113.38γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979490DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.23099.912.896.625529

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 REPLACEMENTTHROUGHOUT3u9h2.219.1824253127799.750.190830.18830.23698RANDOM44.728
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]
-0.72-2.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.493
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg15.13
r_long_range_B_refined9.249
r_long_range_B_other9.246
r_dihedral_angle_1_deg6.81
r_scangle_other5.797
r_mcangle_it4.935
r_mcangle_other4.934
r_scbond_it3.856
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.493
r_dihedral_angle_4_deg18.205
r_dihedral_angle_3_deg15.13
r_long_range_B_refined9.249
r_long_range_B_other9.246
r_dihedral_angle_1_deg6.81
r_scangle_other5.797
r_mcangle_it4.935
r_mcangle_other4.934
r_scbond_it3.856
r_scbond_other3.855
r_mcbond_it3.265
r_mcbond_other3.26
r_angle_refined_deg1.716
r_angle_other_deg0.788
r_chiral_restr0.277
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.001
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 Atoms3303
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms72

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing