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Crystal Structure of the wild-type SAM domain of human Tankyrase-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.2 M magnesium formate
Crystal Properties Matthews coefficient Solvent content 3.78 67.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.322 α = 90 b = 55.101 β = 115.88 c = 92.441 γ = 90
Symmetry Space Group P 1 21 1
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 315 2014-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.03319 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 30 98.4 10.7 6.3 30719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3h8m 2.5 30 29169 1538 98.11 0.17042 0.16822 0.1757 0.21218 0.2187 RANDOM 65.966
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 0.95 -0.95 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 17.885 r_long_range_B_other 13.118 r_long_range_B_refined 13.107 r_scangle_other 11.894 r_dihedral_angle_4_deg 10.711 r_scbond_it 8.733 r_scbond_other 8.731 r_mcangle_other 6.293 r_mcangle_it 6.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.942 r_dihedral_angle_3_deg 17.885 r_long_range_B_other 13.118 r_long_range_B_refined 13.107 r_scangle_other 11.894 r_dihedral_angle_4_deg 10.711 r_scbond_it 8.733 r_scbond_other 8.731 r_mcangle_other 6.293 r_mcangle_it 6.292 r_dihedral_angle_1_deg 5.826 r_mcbond_it 4.932 r_mcbond_other 4.929 r_angle_refined_deg 1.603 r_angle_other_deg 1.068 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3441 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling Coot model building