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Human PARP10 ART domain bound to a phthalazinone-based inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LX6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.586 M NaCl
0.05M MgSO4
0.05M MES pH 6
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.197 α = 90 b = 87.512 β = 104.19 c = 57.524 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 16M 2024-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.976 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.02 55.76 97.5 0.169 0.186 0.985 6.4 5.7 31714
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.05 1.55 1.761 0.37
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 2.02 34.45 29893 1520 96.58 0.18581 0.18384 0.1978 0.22403 0.2311 RANDOM 31.627
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] -1.05 -0.3 -2.4 3.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.613 r_dihedral_angle_2_deg 12.601 r_long_range_B_refined 9.962 r_long_range_B_other 9.925 r_scangle_other 6.959 r_dihedral_angle_1_deg 6.146 r_mcangle_it 4.588 r_mcangle_other 4.587 r_scbond_it 4.522 r_scbond_other 4.521
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.613 r_dihedral_angle_2_deg 12.601 r_long_range_B_refined 9.962 r_long_range_B_other 9.925 r_scangle_other 6.959 r_dihedral_angle_1_deg 6.146 r_mcangle_it 4.588 r_mcangle_other 4.587 r_scbond_it 4.522 r_scbond_other 4.521 r_mcbond_it 3.152 r_mcbond_other 3.13 r_angle_refined_deg 1.58 r_angle_other_deg 0.543 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 3112 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing