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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 0.56 M NaCl
0.05 M MgSO4
0.05 M MES pH 6
Crystal Properties Matthews coefficient Solvent content 2.82 56.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.752 α = 90 b = 88.121 β = 104.38 c = 57.574 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 2024-02-23 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) 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 1.4 47.17 99.9 0.089 0.097 0.037 0.998 11.1 6.8 98126
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 1.4 1.42 100 1.166 1.263 0.481 0.635 6.8
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 1.4 47.17 93170 4879 99.88 0.15561 0.15461 0.1545 0.17497 0.1747 RANDOM 17.409
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] -0.22 -0.06 -0.15 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.44 r_dihedral_angle_2_deg 8.003 r_long_range_B_refined 7.213 r_long_range_B_other 6.924 r_dihedral_angle_1_deg 5.931 r_scangle_other 5.178 r_scbond_it 3.362 r_scbond_other 3.361 r_mcangle_it 2.981 r_mcangle_other 2.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.44 r_dihedral_angle_2_deg 8.003 r_long_range_B_refined 7.213 r_long_range_B_other 6.924 r_dihedral_angle_1_deg 5.931 r_scangle_other 5.178 r_scbond_it 3.362 r_scbond_other 3.361 r_mcangle_it 2.981 r_mcangle_other 2.981 r_angle_refined_deg 1.94 r_mcbond_it 1.905 r_mcbond_other 1.904 r_angle_other_deg 0.683 r_chiral_restr 0.101 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 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 3118 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing