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Crystal Structure of human PARP-1 ART domain bound to inhibitor UKTT-15
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 EVAPORATION 5.6 298 ~20% PEG 3350, 0.2 M ammonium sulfate, 10% DMSO (plus 20% sucrose in cryo), 100 mM sodium citrate pH 5.6
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.662 α = 90 b = 92.662 β = 90 c = 135.341 γ = 120
Symmetry Space Group P 61 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 2018-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.116 ALS 8.3.1
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 1.8 46.33 99.7 0.057 0.062 0.025 0.999 14.9 6.3 32331
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 1.8 1.84 97.9 1.053 1.151 0.454 0.572 6.1
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 1.8 46.37 30669 1647 99.46 0.178 0.1775 0.1882 0.1864 0.1955 RANDOM 39.93
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] -0.91 -0.45 -0.91 2.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.89 r_dihedral_angle_4_deg 16.918 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 7.271 r_angle_refined_deg 1.451 r_angle_other_deg 1.3 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.89 r_dihedral_angle_4_deg 16.918 r_dihedral_angle_3_deg 14.917 r_dihedral_angle_1_deg 7.271 r_angle_refined_deg 1.451 r_angle_other_deg 1.3 r_chiral_restr 0.067 r_bond_refined_d 0.008 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 102 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing PDB_EXTRACT data extraction