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Structure of PARP1 catalytic domain bound to inhibitor BMN 673
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UK0 1UK0, 3L3M experimental model PDB 3L3M 1UK0, 3L3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.2 298 2.1 M AMMONIUM SULFATE, 100mM TRIS, PH 7.2
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.69 α = 90 b = 108.15 β = 90 c = 142 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 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 2.35 19.94 99.6 0.079 17.2 6.9 66890 -3 43.4
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 2.35 2.41 99.4 0.479 3.8
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 1UK0, 3L3M 2.35 19.94 63499 3387 99.63 0.19002 0.18802 0.1918 0.22816 0.2285 RANDOM 41.823
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] -0.01 -0.07 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.699 r_dihedral_angle_4_deg 18.128 r_dihedral_angle_3_deg 14.247 r_long_range_B_refined 6.073 r_long_range_B_other 6.024 r_dihedral_angle_1_deg 5.775 r_scangle_other 4.479 r_mcangle_it 3.56 r_mcangle_other 3.56 r_scbond_it 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.699 r_dihedral_angle_4_deg 18.128 r_dihedral_angle_3_deg 14.247 r_long_range_B_refined 6.073 r_long_range_B_other 6.024 r_dihedral_angle_1_deg 5.775 r_scangle_other 4.479 r_mcangle_it 3.56 r_mcangle_other 3.56 r_scbond_it 2.86 r_scbond_other 2.859 r_mcbond_it 2.308 r_mcbond_other 2.307 r_angle_refined_deg 1.461 r_angle_other_deg 1.255 r_chiral_restr 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 10173 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement PHASER phasing