3P0Q

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 DROP8.527721% PEG3350, 0.2M lithium sulfate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.015α = 90
b = 97.698β = 90
c = 118.885γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-225Mirrors and double crystal monochromator2010-02-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91841BESSY14.2

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
11.93599.60.0650.07920.96.14186541865
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)
11.91.9596.90.530.5063.54.82963

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 3KR71.934.05397713977120941000.174050.174050.172450.20447RANDOM19.444
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]
-0.06-0.880.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.092
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg6.165
r_scangle_it4.657
r_scbond_it2.903
r_mcangle_it2.018
r_angle_refined_deg1.693
r_mcbond_it1.098
r_angle_other_deg0.915
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.092
r_dihedral_angle_4_deg16.98
r_dihedral_angle_3_deg12.964
r_dihedral_angle_1_deg6.165
r_scangle_it4.657
r_scbond_it2.903
r_mcangle_it2.018
r_angle_refined_deg1.693
r_mcbond_it1.098
r_angle_other_deg0.915
r_mcbond_other0.306
r_chiral_restr0.104
r_bond_refined_d0.019
r_gen_planes_refined0.008
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 Atoms3335
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms64

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling