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Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DQY PDB ENTRY 4DQY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 25 mM HEPES, 150 mM sodium chloride, 1 mM EDTA, 0.1 mM TCEP, 6.8% PEG3350, 2% ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.87 57.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.16 α = 90 b = 114.23 β = 90 c = 294.24 γ = 90
Symmetry Space Group P 21 21 21
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 2013-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.65 50 25245 24937
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.65
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 PDB ENTRY 4DQY 3.65 20 23595 1250 98.1 0.30022 0.29845 0.2978 0.33424 0.3428 RANDOM 257.215
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] -1.03 9.67 -8.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_4_deg 11.394 r_dihedral_angle_1_deg 4.338 r_long_range_B_refined 4.105 r_long_range_B_other 4.105 r_mcangle_it 2.114 r_mcangle_other 2.114 r_scangle_other 1.226 r_mcbond_it 1.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 14.893 r_dihedral_angle_4_deg 11.394 r_dihedral_angle_1_deg 4.338 r_long_range_B_refined 4.105 r_long_range_B_other 4.105 r_mcangle_it 2.114 r_mcangle_other 2.114 r_scangle_other 1.226 r_mcbond_it 1.126 r_mcbond_other 1.126 r_angle_other_deg 0.86 r_angle_refined_deg 0.774 r_scbond_it 0.605 r_scbond_other 0.605 r_chiral_restr 0.059 r_bond_refined_d 0.004 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 10666 Nucleic Acid Atoms 1060 Solvent Atoms Heterogen Atoms 26
Software Software Software Name Purpose CBASS data collection REFMAC refinement xia2 data reduction xia2 data scaling