3KR7

Human tankyrase 2 - catalytic PARP domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2RF5PDB ENTRY 2RF5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527715% PEG 3350, 0.2M LithiumSulfate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4249.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.847α = 90
b = 66.847β = 90
c = 118.047γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2009-10-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.96860DiamondI03

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
11.95451000.10.05718.513.62022920229
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)
11.9521000.5780.271514.31471

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 2RF51.9544.24192171921710121000.180870.180870.178830.21852RANDOM20.92
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]
0.050.05-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.196
r_dihedral_angle_4_deg20.107
r_dihedral_angle_3_deg13.287
r_dihedral_angle_1_deg6.201
r_scangle_it4.181
r_scbond_it2.599
r_mcangle_it1.758
r_angle_refined_deg1.539
r_mcbond_it0.966
r_angle_other_deg0.895
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.196
r_dihedral_angle_4_deg20.107
r_dihedral_angle_3_deg13.287
r_dihedral_angle_1_deg6.201
r_scangle_it4.181
r_scbond_it2.599
r_mcangle_it1.758
r_angle_refined_deg1.539
r_mcbond_it0.966
r_angle_other_deg0.895
r_mcbond_other0.247
r_chiral_restr0.096
r_bond_refined_d0.017
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1677
Nucleic Acid Atoms
Solvent Atoms193
Heterogen Atoms23

Software

Software
Software NamePurpose
DNAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling