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Crystal structure of human poly(ADP-ribose) polymerase 15, catalytic fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PQF PDB entry 2PQF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 20% PEG 3350, 0.2M Ammonium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.21 α = 90 b = 68.12 β = 90 c = 158.28 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 MARMOSAIC 225 mm CCD Si mirrors 2007-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 0.97908 MAX II I911-3
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 20 99.2 0.138 0.186 9.7 4.7 25446 25446
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 2.4 98.7 0.568 0.587 3.2 4.4 5711
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 2PQF 2.2 19.78 24170 24170 1272 100 0.18253 0.18253 0.17935 0.179 0.2434 0.2408 RANDOM 24.401
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] -0.37 0.25 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.244 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 14.508 r_dihedral_angle_1_deg 7.036 r_scangle_it 5.232 r_scbond_it 3.565 r_mcangle_it 2.443 r_angle_refined_deg 1.541 r_mcbond_it 1.343 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.244 r_dihedral_angle_4_deg 19.074 r_dihedral_angle_3_deg 14.508 r_dihedral_angle_1_deg 7.036 r_scangle_it 5.232 r_scbond_it 3.565 r_mcangle_it 2.443 r_angle_refined_deg 1.541 r_mcbond_it 1.343 r_nbtor_refined 0.307 r_nbd_refined 0.2 r_symmetry_hbond_refined 0.178 r_symmetry_vdw_refined 0.177 r_xyhbond_nbd_refined 0.158 r_chiral_restr 0.1 r_metal_ion_refined 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3158 Nucleic Acid Atoms Solvent Atoms 288 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling MOLREP phasing