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Complex structure of human tankyrase 2 with nicotinamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2 M LiSO4, 0.1 M Tris HCl
22 % PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.43 49.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.25 α = 90 b = 97.75 β = 90 c = 119.16 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2011-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.07227 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.75 50 100 0.068 18.7 7.2 53905 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.8 100 0.691 3.05 7.3 28656
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3KR7 1.75 45.22 51211 51211 2695 100 0.16741 0.16581 0.19741 0.1972 RANDOM 17.989
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_3_deg 12.525 r_dihedral_angle_1_deg 6.257 r_scangle_it 4.524 r_scbond_it 2.773 r_mcangle_it 1.886 r_angle_refined_deg 1.564 r_mcbond_it 1.032 r_angle_other_deg 0.894
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.91 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_3_deg 12.525 r_dihedral_angle_1_deg 6.257 r_scangle_it 4.524 r_scbond_it 2.773 r_mcangle_it 1.886 r_angle_refined_deg 1.564 r_mcbond_it 1.032 r_angle_other_deg 0.894 r_mcbond_other 0.289 r_chiral_restr 0.092 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.001 r_bond_other_d 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 Atoms Number Protein Atoms 3346 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 60
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling