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The crystal structure of a helical domain deleted PARP1 in complex with isoindolinone based inhibitor.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BHV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 35% PEG2000 MME, 0.2M KSC and 0.1M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.99 38.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.8 α = 109.1 b = 74.84 β = 99.1 c = 83.45 γ = 90.58
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 PILATUS 6M 2023-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 0.979 SPring-8 BL45XU
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 3.02 45.31 98.9 0.09 8.9 3.5 16544
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 3.02 3.2 0.424
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.02 45.31 15220 755 95.5 0.24416 0.24184 0.2399 0.29154 0.294 RANDOM 69.333
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] -5.41 2.88 1.71 -0.32 2.9 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.038 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.477 r_long_range_B_refined 1.868 r_long_range_B_other 1.864 r_angle_refined_deg 1.231 r_angle_other_deg 1.008 r_mcangle_it 0.83 r_mcangle_other 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.038 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 6.477 r_long_range_B_refined 1.868 r_long_range_B_other 1.864 r_angle_refined_deg 1.231 r_angle_other_deg 1.008 r_mcangle_it 0.83 r_mcangle_other 0.83 r_scangle_other 0.588 r_mcbond_it 0.446 r_mcbond_other 0.446 r_scbond_it 0.297 r_scbond_other 0.297 r_chiral_restr 0.036 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 7333 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement MOLREP phasing XDS data reduction XDS data scaling