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Human poly(adp-ribose) polymerase 15 (ARTD7, BAL3), macro domain 2 in complex with adenosine-5-diphosphoribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPV PDB ENTRY 1SPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 20% PEG6000, 0.1M NA-ACETATE, 0.2M NaCl, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.26 45.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.102 α = 90 b = 91.187 β = 90 c = 62.851 γ = 90
Symmetry Space Group C 2 2 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 MAR CCD 165 mm MIRRORS 2009-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 2.2 35 100 0.127 0.12 13.9 7.2 10255 10255
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 2.2 2.26 100 0.553 0.417 4.4 7.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1SPV 2.2 34.05 9742 9742 513 100 0.17648 0.17648 0.17327 0.1769 0.23823 0.2382 RANDOM 19.384
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] 2.02 -0.66 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 5.754 r_scangle_it 4.23 r_scbond_it 2.538 r_mcangle_it 1.63 r_angle_refined_deg 1.586 r_angle_other_deg 0.934 r_mcbond_it 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.357 r_dihedral_angle_4_deg 18.914 r_dihedral_angle_3_deg 15 r_dihedral_angle_1_deg 5.754 r_scangle_it 4.23 r_scbond_it 2.538 r_mcangle_it 1.63 r_angle_refined_deg 1.586 r_angle_other_deg 0.934 r_mcbond_it 0.88 r_mcbond_other 0.197 r_chiral_restr 0.097 r_bond_refined_d 0.018 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1336 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 36
Software Software Software Name Purpose MxCuBE data collection BALBES phasing REFMAC refinement XDS data reduction XSCALE data scaling