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Human PARP1 ART domain bound to NAD+ analog benzamide adenine dinucleotide and ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9BPY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.456 α = 98.31 b = 74.906 β = 105.04 c = 85.115 γ = 105.38
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 2024-04-02 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 3 29.77 93.9 0.062 0.072 0.037 0.998 15.1 3.6 18710
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 3 3.18 86 0.578 0.683 0.356 0.918 3.4
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 25 17490 918 92.38 0.29363 0.29249 0.2773 0.31655 0.3041 RANDOM 109.948
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] -5.68 6.84 -2.27 13.26 2.05 -10.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.232 r_dihedral_angle_1_deg 6.666 r_long_range_B_refined 5.859 r_long_range_B_other 5.858 r_dihedral_angle_2_deg 5.515 r_mcangle_it 3.581 r_mcangle_other 3.581 r_scangle_other 2.899 r_mcbond_it 2.048 r_mcbond_other 2.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.232 r_dihedral_angle_1_deg 6.666 r_long_range_B_refined 5.859 r_long_range_B_other 5.858 r_dihedral_angle_2_deg 5.515 r_mcangle_it 3.581 r_mcangle_other 3.581 r_scangle_other 2.899 r_mcbond_it 2.048 r_mcbond_other 2.047 r_scbond_it 1.565 r_scbond_other 1.563 r_angle_refined_deg 0.921 r_angle_other_deg 0.316 r_chiral_restr 0.041 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_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 7 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing