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Human PARP14 (ARTD8), catalytic fragment in complex with inhibitor H10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4F1L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 22.5% PEG3350, 0.225M Sodium malonate
Crystal Properties Matthews coefficient Solvent content 2.75 55.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.032 α = 90 b = 83.032 β = 90 c = 122.08 γ = 120
Symmetry Space Group P 31 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 2015-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97999 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.17 46.5 99.7 0.096 0.998 14 9.5 26408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.17 2.3 98.2 1.13 0.754 2 8.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4F1L 2.17 46.5 24403 2004 99.65 0.19703 0.19535 0.1956 0.21783 0.2213 RANDOM 61.287
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] -31.74 -31.74 63.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 23.782 r_dihedral_angle_3_deg 16.829 r_long_range_B_refined 10.628 r_long_range_B_other 10.627 r_dihedral_angle_1_deg 7.753 r_mcangle_it 7.377 r_mcangle_other 7.375 r_scangle_other 7.341 r_mcbond_it 5.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.279 r_dihedral_angle_4_deg 23.782 r_dihedral_angle_3_deg 16.829 r_long_range_B_refined 10.628 r_long_range_B_other 10.627 r_dihedral_angle_1_deg 7.753 r_mcangle_it 7.377 r_mcangle_other 7.375 r_scangle_other 7.341 r_mcbond_it 5.162 r_mcbond_other 5.157 r_scbond_it 4.945 r_scbond_other 4.944 r_angle_refined_deg 1.751 r_angle_other_deg 1.271 r_chiral_restr 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 2987 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing