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The Crystal Structure of PARP12 from Biortus.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6V3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2M NH4Ac, 0.1M Na3 Citrate pH5.2, 30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.21 44.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.94 α = 90 b = 74.93 β = 113.835 c = 61.49 γ = 90
Symmetry Space Group C 1 2 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 2023-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1 SPring-8 BL45XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 46.6 98.7 0.079 10.8 3.4 38860
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.728
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 1.75 46.6 38859 1898 98.69 0.165 0.1636 0.1725 0.1942 0.2052 27.829
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] -1.141 0.366 0.068 0.539
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.744 r_dihedral_angle_3_deg 11.441 r_lrange_it 6.435 r_lrange_other 6.334 r_dihedral_angle_2_deg 6.273 r_dihedral_angle_1_deg 6.237 r_scangle_it 4.547 r_scangle_other 4.546 r_mcangle_it 3.342 r_mcangle_other 3.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.744 r_dihedral_angle_3_deg 11.441 r_lrange_it 6.435 r_lrange_other 6.334 r_dihedral_angle_2_deg 6.273 r_dihedral_angle_1_deg 6.237 r_scangle_it 4.547 r_scangle_other 4.546 r_mcangle_it 3.342 r_mcangle_other 3.341 r_scbond_it 2.818 r_scbond_other 2.817 r_mcbond_it 2.142 r_mcbond_other 2.116 r_angle_refined_deg 1.116 r_angle_other_deg 0.396 r_nbd_refined 0.205 r_nbtor_refined 0.188 r_symmetry_nbd_other 0.185 r_nbd_other 0.144 r_symmetry_nbd_refined 0.132 r_xyhbond_nbd_refined 0.119 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.057 r_chiral_restr_other 0.051 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2970 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing