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Human PARP1 ART domain bound to NAD+ analogs benzamide adenine dinucleotide and carba-NAD+
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 295 PARP1 ART (30 mg/ml) was crystallized in the presence of 1.6 mM BAD in 24 to 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.664 α = 98.49 b = 74.142 β = 105.16 c = 85.182 γ = 104.8
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 2024-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18 CLSI 08B1-1
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 2.8 19.95 97.9 0.088 0.099 0.044 0.998 12.4 4.9 23920
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 2.8 2.95 97.3 1.314 1.475 0.661 0.608 4.8
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 2.8 19.95 22735 1182 97.86 0.22588 0.22428 0.2235 0.25758 0.2575 RANDOM 100.99
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] -3.23 0.32 -0.14 1.46 1.12 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.217 r_dihedral_angle_2_deg 8.002 r_dihedral_angle_1_deg 6.748 r_long_range_B_refined 5.424 r_long_range_B_other 5.424 r_mcangle_it 3.246 r_mcangle_other 3.246 r_scangle_other 2.681 r_mcbond_other 1.876 r_mcbond_it 1.875
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.217 r_dihedral_angle_2_deg 8.002 r_dihedral_angle_1_deg 6.748 r_long_range_B_refined 5.424 r_long_range_B_other 5.424 r_mcangle_it 3.246 r_mcangle_other 3.246 r_scangle_other 2.681 r_mcbond_other 1.876 r_mcbond_it 1.875 r_scbond_it 1.514 r_scbond_other 1.514 r_angle_refined_deg 0.882 r_angle_other_deg 0.297 r_chiral_restr 0.039 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 7422 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction