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Crystal Structure of human PARP-1 CAT domain bound to inhibitor rucaparib
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 8 298 2M Ammonium Sulfate, 5% PEG 400, 100 mM Tris
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.267 α = 90 b = 107.902 β = 90 c = 142.845 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 270 2014-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 12.3.1 1.1158 ALS 12.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 47.92 99.8 0.089 0.094 0.028 0.998 16.3 11.7 94458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.14 100 1.336 1.394 0.395 0.778 12.3
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 2.1 20 89014 4674 99.1 0.2402 0.2391 0.2447 0.2607 0.2656 RANDOM 55.022
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] -0.44 1.06 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.725 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_4_deg 12.721 r_dihedral_angle_1_deg 6.23 r_angle_refined_deg 1.237 r_angle_other_deg 1.123 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.725 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_4_deg 12.721 r_dihedral_angle_1_deg 6.23 r_angle_refined_deg 1.237 r_angle_other_deg 1.123 r_chiral_restr 0.051 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10786 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 159
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction