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PARP10 catalytic domain in complex with OUL499
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 7 293 0.1M HEPES, 10% w/v PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.56 52.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.59 α = 102.572 b = 71.65 β = 96.375 c = 131.46 γ = 90.006
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 PILATUS3 6M 2024-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
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 2.75 50 90.9 0.053 0.075 0.996 10.01 1.7 40627
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 2.75 2.82 60.7 0.335 0.473 0.739 1.5
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.75 48.321 40627 2032 90.911 0.217 0.214 0.2141 0.2645 0.2644 49.846
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] -1.057 0.504 0.343 0.156 -1.006 1.131
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.983 r_dihedral_angle_4_deg 20.057 r_dihedral_angle_3_deg 17.561 r_lrange_it 11.047 r_lrange_other 11.047 r_scangle_it 8.471 r_scangle_other 8.47 r_mcangle_other 7.91 r_mcangle_it 7.908 r_dihedral_angle_1_deg 7.675
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.983 r_dihedral_angle_4_deg 20.057 r_dihedral_angle_3_deg 17.561 r_lrange_it 11.047 r_lrange_other 11.047 r_scangle_it 8.471 r_scangle_other 8.47 r_mcangle_other 7.91 r_mcangle_it 7.908 r_dihedral_angle_1_deg 7.675 r_scbond_it 5.651 r_scbond_other 5.65 r_mcbond_it 5.404 r_mcbond_other 5.397 r_angle_refined_deg 1.69 r_angle_other_deg 1.21 r_symmetry_xyhbond_nbd_other 0.436 r_nbd_other 0.226 r_nbd_refined 0.206 r_symmetry_nbd_other 0.187 r_nbtor_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.166 r_xyhbond_nbd_refined 0.153 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.066 r_ncsr_local_group_21 0.066 r_ncsr_local_group_17 0.058 r_ncsr_local_group_20 0.058 r_ncsr_local_group_6 0.057 r_ncsr_local_group_9 0.056 r_ncsr_local_group_3 0.055 r_ncsr_local_group_8 0.054 r_ncsr_local_group_11 0.054 r_ncsr_local_group_1 0.053 r_ncsr_local_group_5 0.053 r_ncsr_local_group_24 0.053 r_ncsr_local_group_10 0.052 r_ncsr_local_group_12 0.051 r_ncsr_local_group_28 0.051 r_ncsr_local_group_4 0.049 r_ncsr_local_group_13 0.049 r_ncsr_local_group_14 0.048 r_ncsr_local_group_23 0.048 r_ncsr_local_group_19 0.047 r_ncsr_local_group_16 0.046 r_ncsr_local_group_22 0.046 r_ncsr_local_group_26 0.046 r_ncsr_local_group_27 0.045 r_ncsr_local_group_15 0.044 r_ncsr_local_group_2 0.04 r_ncsr_local_group_7 0.039 r_ncsr_local_group_18 0.037 r_ncsr_local_group_25 0.035 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11992 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 168
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing