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Human Artd8 (Parp14, Bal2) - catalytic domain in complex with inhibitor A16(Z)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SMI PDB ENTRY 3SMI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.9 293 20% (w/v) polyethylene glycol (PEG) 3350, 0.2 M sodium nitrate, 0.1 M Bis-Tris, 1.3mM A16, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.58 52.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.649 α = 60.12 b = 81.894 β = 78.32 c = 83.187 γ = 80.31
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 RAYONIX MX-225 mirrors 2011-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.9 35 96.7 0.066 12.1 3.9 67716 67716
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 1.9 1.95 95.7 0.521 3.8 3.9 4926
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 (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 3SMI 1.9 34.89 64330 64330 3386 100 0.1988 0.19666 0.2007 0.23939 0.2421 RANDOM 24.939
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] 0.5 -0.09 0.08 0.78 0.51 -1.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.521 r_dihedral_angle_4_deg 23.009 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_1_deg 7.009 r_scangle_it 4.033 r_scbond_it 2.531 r_mcangle_it 1.78 r_angle_refined_deg 1.652 r_mcbond_it 1.028 r_angle_other_deg 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.521 r_dihedral_angle_4_deg 23.009 r_dihedral_angle_3_deg 14.838 r_dihedral_angle_1_deg 7.009 r_scangle_it 4.033 r_scbond_it 2.531 r_mcangle_it 1.78 r_angle_refined_deg 1.652 r_mcbond_it 1.028 r_angle_other_deg 0.973 r_mcbond_other 0.359 r_chiral_restr 0.103 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5986 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 76
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling