3MHK

Human tankyrase 2 - catalytic PARP domain in complex with 2-(2-pyridyl)-7,8-dihydro-5h-thiino[4,3-d]pyrimidin-4-ol


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KR7PDB ENTRY 3KR7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52771.34M dipotassium hydrogen phosphate, 0.06M sodium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5952.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.484α = 90
b = 92.484β = 90
c = 53.506γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rliquid nitrogen cooled channel-cut silicon monochromator and cylindrical grazing incidence mirror2009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97908ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
12.346.2499.10.0970.06522.210.91193211932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.3697.80.5570.2875.910.5880

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 3KR72.346.2411335113355971000.179480.179480.176910.22725RANDOM17.789
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]
0.350.180.35-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_3_deg15.277
r_dihedral_angle_4_deg13.706
r_dihedral_angle_1_deg6.127
r_scangle_it3.254
r_scbond_it1.969
r_mcangle_it1.353
r_angle_refined_deg1.308
r_angle_other_deg0.808
r_mcbond_it0.687
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_3_deg15.277
r_dihedral_angle_4_deg13.706
r_dihedral_angle_1_deg6.127
r_scangle_it3.254
r_scbond_it1.969
r_mcangle_it1.353
r_angle_refined_deg1.308
r_angle_other_deg0.808
r_mcbond_it0.687
r_mcbond_other0.127
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1686
Nucleic Acid Atoms
Solvent Atoms70
Heterogen Atoms36

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling