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Catalytic domain of human PARP15 in complex with BAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 278 20% (w/v) PEG 3350, 0.2 M ammonium chloride
No pH buffer in the crystallisation solution; protein stock contained 30 mM Hepes at pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.15 α = 90 b = 68.51 β = 90 c = 159.61 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER2 X 9M 2024-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96863 ESRF ID30B
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 1.9 43.483 99.9 0.117 0.122 0.033 0.999 13.7 13.2 39921 28.3
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 1.9 1.949 100 0.882 0.923 0.268 0.838 2.1 11.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 43.483 39921 1849 99.872 0.184 0.1819 0.1907 0.2197 0.2261 Random selection 31.959
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] -1.914 0.473 1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.781 r_dihedral_angle_2_deg 13.585 r_dihedral_angle_3_deg 11.407 r_lrange_it 7.115 r_lrange_other 7.036 r_dihedral_angle_1_deg 6.694 r_scangle_it 4.78 r_scangle_other 4.779 r_mcangle_other 4.082 r_mcangle_it 4.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.781 r_dihedral_angle_2_deg 13.585 r_dihedral_angle_3_deg 11.407 r_lrange_it 7.115 r_lrange_other 7.036 r_dihedral_angle_1_deg 6.694 r_scangle_it 4.78 r_scangle_other 4.779 r_mcangle_other 4.082 r_mcangle_it 4.08 r_scbond_it 3.08 r_scbond_other 3.08 r_mcbond_it 2.598 r_mcbond_other 2.598 r_angle_refined_deg 1.455 r_angle_other_deg 0.51 r_dihedral_angle_other_2_deg 0.364 r_nbd_refined 0.209 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.151 r_nbd_other 0.146 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.117 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.069 r_symmetry_xyhbond_nbd_other 0.054 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3135 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 53
Software Software Software Name Purpose MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building REFMAC refinement