3P0N

Human Tankyrase 2 - Catalytic PARP domain in complex with an inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827721% PEG3350, 0.2M ammonium sulfate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4449.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.3α = 90
b = 98.214β = 90
c = 118.684γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-12-17MSINGLE 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
11.945.3899.90.0620.0423.77.24220842208
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)
11.91.9599.70.1830.12410.26.93067

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 3KR71.945.38400974009721111000.161350.161350.159530.19501RANDOM14.627
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]
-0.03-0.740.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.572
r_dihedral_angle_4_deg16.992
r_dihedral_angle_3_deg13.277
r_dihedral_angle_1_deg6.158
r_scangle_it5.135
r_scbond_it3.197
r_mcangle_it2.096
r_angle_refined_deg1.737
r_mcbond_it1.15
r_angle_other_deg0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.572
r_dihedral_angle_4_deg16.992
r_dihedral_angle_3_deg13.277
r_dihedral_angle_1_deg6.158
r_scangle_it5.135
r_scbond_it3.197
r_mcangle_it2.096
r_angle_refined_deg1.737
r_mcbond_it1.15
r_angle_other_deg0.93
r_mcbond_other0.332
r_chiral_restr0.102
r_bond_refined_d0.019
r_gen_planes_refined0.009
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 Atoms3333
Nucleic Acid Atoms
Solvent Atoms489
Heterogen Atoms63

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling