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Human ARTD3 (PARP3) - Catalytic domain in complex with inhibitor ME0328
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FHB PDB ENTRY 3FHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 1.8M DL-Malic Acid, 0.1M Bis-tris-propane, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.664 α = 90 b = 56.742 β = 112.74 c = 56.977 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r focusing mirrors 2011-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.99190 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.8 30 99.4 0.079 0.08 21.5 7.4 29828 29828
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 97.6 0.568 0.441 21.5 7.1 2148
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 3FHB 1.8 28.37 28335 28335 1492 100 0.1643 0.1643 0.16222 0.1701 0.20333 0.2102 RANDOM 17.246
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] 0.94 0.16 -0.75 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.486 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.558 r_scbond_it 2.902 r_mcangle_it 1.778 r_angle_refined_deg 1.549 r_mcbond_it 1.08 r_angle_other_deg 0.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.486 r_dihedral_angle_4_deg 18.733 r_dihedral_angle_3_deg 12.537 r_dihedral_angle_1_deg 6.487 r_scangle_it 4.558 r_scbond_it 2.902 r_mcangle_it 1.778 r_angle_refined_deg 1.549 r_mcbond_it 1.08 r_angle_other_deg 0.908 r_mcbond_other 0.3 r_chiral_restr 0.093 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 28
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling