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Human poly(ADP-ribose) polymerase 2, catalytic fragment in complex with an inhibitor ABT-888
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KCZ PDB ENTRY 3KCZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 25% PEG 3350, 0.1M Tris, 0.25M NaCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.134 α = 90 b = 134.611 β = 117.68 c = 58.314 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 2009-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9789 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 41 99.3 0.096 0.125 11.5 3.8 57455 57455
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2 99.7 0.568 0.582 2.7 3.8 4253
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3KCZ 1.95 40.97 54581 54581 2873 100 0.18157 0.18157 0.17889 0.23192 0.2291 RANDOM 18.149
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 0.29 0.18 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.663 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_1_deg 6.102 r_scangle_it 4.334 r_scbond_it 2.661 r_mcangle_it 1.665 r_angle_refined_deg 1.488 r_angle_other_deg 0.919 r_mcbond_it 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.663 r_dihedral_angle_4_deg 18.662 r_dihedral_angle_3_deg 13.772 r_dihedral_angle_1_deg 6.102 r_scangle_it 4.334 r_scbond_it 2.661 r_mcangle_it 1.665 r_angle_refined_deg 1.488 r_angle_other_deg 0.919 r_mcbond_it 0.912 r_mcbond_other 0.236 r_chiral_restr 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5562 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 48
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling