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PARP9 Macro Domain 2 in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 0.1 MES, 0.2M Ammonium chloride, 20% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.37 48.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.428 α = 90 b = 73.827 β = 116.9 c = 58.465 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 PILATUS 6M 2024-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.9655 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.5 73.83 92.8 0.996 7.9 3.1 13136
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.6 0.714 1.3
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 2.5 52.19 11763 1356 92.7 0.20227 0.19727 0.2093 0.24602 0.2547 RANDOM 77.358
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] 2.9 0.96 -3.01 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.45 r_dihedral_angle_2_deg 13.573 r_long_range_B_refined 9.824 r_long_range_B_other 9.822 r_dihedral_angle_1_deg 6.628 r_scangle_other 6.351 r_mcangle_it 5.357 r_mcangle_other 5.357 r_scbond_it 4.009 r_scbond_other 4.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.45 r_dihedral_angle_2_deg 13.573 r_long_range_B_refined 9.824 r_long_range_B_other 9.822 r_dihedral_angle_1_deg 6.628 r_scangle_other 6.351 r_mcangle_it 5.357 r_mcangle_other 5.357 r_scbond_it 4.009 r_scbond_other 4.008 r_mcbond_it 3.334 r_mcbond_other 3.333 r_angle_refined_deg 1.69 r_angle_other_deg 0.511 r_chiral_restr 0.066 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 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 2863 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing