5AEH | pdb_00005aeh

Crystal structure of human tankyrase 2 in complex with OD332


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3U9HPDB ENTRY 3U9H

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
190.1M BICINE PH9.0, 20% PEG6K
Crystal Properties
Matthews coefficientSolvent content
2.142

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.13α = 90
b = 76.07β = 90
c = 147.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMIRRORS2015-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-1DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.852099.30.199.76.540278-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.92991.26.7

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3U9H1.8519.8538264201499.280.218770.216030.220.270660.28RANDOM35.354
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]
0.214.41-4.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.272
r_dihedral_angle_4_deg15.993
r_dihedral_angle_3_deg15.431
r_dihedral_angle_1_deg7.112
r_mcangle_it4.132
r_scbond_it3.084
r_mcbond_it2.678
r_mcbond_other2.677
r_angle_refined_deg1.73
r_angle_other_deg1.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.272
r_dihedral_angle_4_deg15.993
r_dihedral_angle_3_deg15.431
r_dihedral_angle_1_deg7.112
r_mcangle_it4.132
r_scbond_it3.084
r_mcbond_it2.678
r_mcbond_other2.677
r_angle_refined_deg1.73
r_angle_other_deg1.039
r_chiral_restr0.092
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3306
Nucleic Acid Atoms
Solvent Atoms231
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing