5ADR | pdb_00005adr

Crystal structure of human tankyrase 2 in complex with OD38


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.50.2 M LISO4, 0.1 M TRIS HCL, 22 % PEG 3350, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.57α = 90
b = 65.57β = 90
c = 121.92γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELTOROIDAL MIRRORS2013-02-09MSINGLE 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
12.13099.50.167.86.716121-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.151000.722.47.1

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 DIFFRACTIONOTHERTHROUGHOUTNONE2.129.321531480699.530.189730.187250.190.238750.24RANDOM27.043
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]
-0.11-0.110.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.093
r_dihedral_angle_4_deg17.19
r_dihedral_angle_3_deg12.217
r_dihedral_angle_1_deg6.611
r_angle_refined_deg1.541
r_angle_other_deg0.823
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.093
r_dihedral_angle_4_deg17.19
r_dihedral_angle_3_deg12.217
r_dihedral_angle_1_deg6.611
r_angle_refined_deg1.541
r_angle_other_deg0.823
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.003
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
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 Atoms1670
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling