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Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor DR2313
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PA9 PDB entry 2PA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.9 M DL-Malic acid, 0.1 M Bis-Tris propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.06 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.91 α = 90 b = 57.33 β = 112.36 c = 56.26 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 315 Mirrors 2007-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0000 ESRF ID29
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 2.1 20 99.6 0.105 15.22 7.4 18978 18978 24.9
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 2.1 2.2 100 0.45 4.64 7.5 2442
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 2PA9 2.1 19.98 18027 18027 949 100 0.17758 0.17758 0.17421 0.1735 0.24197 0.2403 RANDOM 25.402
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] 0.29 0.15 -0.19 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.989 r_dihedral_angle_4_deg 17.77 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 5.781 r_scangle_it 2.201 r_scbond_it 1.397 r_angle_refined_deg 1.13 r_mcangle_it 0.941 r_mcbond_it 0.568 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.989 r_dihedral_angle_4_deg 17.77 r_dihedral_angle_3_deg 12.782 r_dihedral_angle_1_deg 5.781 r_scangle_it 2.201 r_scbond_it 1.397 r_angle_refined_deg 1.13 r_mcangle_it 0.941 r_mcbond_it 0.568 r_nbtor_refined 0.297 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.132 r_symmetry_hbond_refined 0.126 r_chiral_restr 0.071 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2769 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing