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Crystal Structure of human PARP-1 CAT domain bound to inhibitor UKTT15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 2M Ammonium Sulfate, Bis-Tris pH6.5
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 139.701 α = 90 b = 129.751 β = 111.36 c = 102.72 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 S 6M 2018-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.1158 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 2.8 95.664 95.4 0.152 0.17 0.076 5.3 4.6 39944 39944
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 95.5 0.709 0.709 0.799 0.359 1.1 4.5
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 5ds3 2.8 20 37777 2021 94.69 0.2857 0.2843 0.2902 0.3122 0.3178 RANDOM 90.658
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] 1.51 2.05 -2.25 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_3_deg 20.359 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_1_deg 8.746 r_angle_refined_deg 1.471 r_angle_other_deg 1.091 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.44 r_dihedral_angle_3_deg 20.359 r_dihedral_angle_4_deg 16.876 r_dihedral_angle_1_deg 8.746 r_angle_refined_deg 1.471 r_angle_other_deg 1.091 r_chiral_restr 0.057 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10712 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 204
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing