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Crystal Structure of human PARP-1 ART domain bound inhibitor UTT63
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BHV PDBID 6BHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 7.5 298 ~20% PEG 3350, 0.2 M ammonium sulfate or sodium citrate, 100 mM Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.51 51.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.503 α = 90 b = 93.503 β = 90 c = 137.948 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2018-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.5 47.78 100 0.041 0.041 0.008 1 36.7 24.1 49081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.4 1.36 1.408 0.36 0.783 14.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDBID 6BHV 1.5 47.78 46561 2495 99.96 0.1306 0.1291 0.158 0.185 RANDOM 32.831
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] 0.92 0.92 -1.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.89 r_sphericity_free 28.704 r_sphericity_bonded 17.868 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 6.702 r_rigid_bond_restr 2.227 r_angle_refined_deg 1.337 r_angle_other_deg 0.937 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.89 r_sphericity_free 28.704 r_sphericity_bonded 17.868 r_dihedral_angle_4_deg 14.675 r_dihedral_angle_3_deg 13.07 r_dihedral_angle_1_deg 6.702 r_rigid_bond_restr 2.227 r_angle_refined_deg 1.337 r_angle_other_deg 0.937 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1895 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 67
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction