☰ Navigation Tabs
Human PARP-1 bound to NAD+ analog benzamide adenine dinucleotide (BAD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PARP-1 CATdeltaHD (30 mg/ml) was crystallized in the presence of 1.6 mM BAD in 24 to 29% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.15 42.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.51 α = 98.66 b = 75.356 β = 104.94 c = 85.607 γ = 106.73
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 210r 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.008 ALS 12.3.1
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 2.3 50 97.8 13.2 4.8 43372
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 5DS3 2.3 20 41185 2138 97.64 0.19901 0.19771 0.2017 0.22233 0.2267 RANDOM 74.854
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] 0.86 0.08 -0.84 2.68 0.57 -2.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 20.661 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 6.647 r_long_range_B_refined 5.388 r_long_range_B_other 5.384 r_scangle_other 2.905 r_mcangle_it 2.888 r_mcangle_other 2.887 r_mcbond_it 1.769
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.854 r_dihedral_angle_4_deg 20.661 r_dihedral_angle_3_deg 14.966 r_dihedral_angle_1_deg 6.647 r_long_range_B_refined 5.388 r_long_range_B_other 5.384 r_scangle_other 2.905 r_mcangle_it 2.888 r_mcangle_other 2.887 r_mcbond_it 1.769 r_mcbond_other 1.767 r_scbond_it 1.738 r_scbond_other 1.738 r_angle_refined_deg 1.489 r_angle_other_deg 0.918 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 7422 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing