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Human PARP14 (ARTD8), catalytic fragment in complex with RBN012759
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SMJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 0.2 M Ammonium sulfate; 0.1 M tri-Sodium citrate pH 5.6; 25 % w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.01 59.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.5 α = 90 b = 84.05 β = 116.02 c = 80.89 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 PILATUS3 6M 2019-08-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 2.66 42.06 98.8 0.117 7.6 4 13344 43.163
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 2.66 2.79 98.5 0.582 2 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3smj 2.66 42.06 13344 689 96.48 0.24825 0.24591 0.29596 0.2896 RANDOM 43.163
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] 4.8 -2.19 0.54 -2.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_1_deg 6.601 r_long_range_B_refined 6.18 r_long_range_B_other 6.179 r_mcangle_it 3.468 r_mcangle_other 3.467 r_scangle_other 2.89 r_mcbond_it 1.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 19.315 r_dihedral_angle_3_deg 13.594 r_dihedral_angle_1_deg 6.601 r_long_range_B_refined 6.18 r_long_range_B_other 6.179 r_mcangle_it 3.468 r_mcangle_other 3.467 r_scangle_other 2.89 r_mcbond_it 1.964 r_mcbond_other 1.964 r_scbond_it 1.596 r_scbond_other 1.596 r_angle_refined_deg 1.241 r_angle_other_deg 1.077 r_chiral_restr 0.041 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2993 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing