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PARP9 Macro Domain 2 in complex with ADPr
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M Succinic acid, 15% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.143 α = 90 b = 52.143 β = 90 c = 132.158 γ = 90
Symmetry Space Group P 43 21 2
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 2024-04-26 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 1.3 40.93 99.4 0.999 17 6.4 45496
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 1.3 1.32 0.698
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 1.3 40.97 43241 2255 99.26 0.13517 0.13325 0.1343 0.17313 0.1736 RANDOM 19.498
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] 1.69 1.69 -3.38
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.871 r_long_range_B_other 12.5 r_dihedral_angle_3_deg 12.007 r_scangle_other 9.547 r_scbond_it 6.969 r_scbond_other 6.965 r_mcangle_other 6.383 r_mcangle_it 6.37 r_dihedral_angle_1_deg 5.693 r_mcbond_it 4.746
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 13.871 r_long_range_B_other 12.5 r_dihedral_angle_3_deg 12.007 r_scangle_other 9.547 r_scbond_it 6.969 r_scbond_other 6.965 r_mcangle_other 6.383 r_mcangle_it 6.37 r_dihedral_angle_1_deg 5.693 r_mcbond_it 4.746 r_mcbond_other 4.703 r_rigid_bond_restr 3.902 r_dihedral_angle_2_deg 3.225 r_angle_refined_deg 1.747 r_angle_other_deg 0.605 r_chiral_restr 0.098 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1518 Nucleic Acid Atoms Solvent Atoms 211 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing