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Structure of ARTD2/PARP2 WGR domain bound to double stranded DNA with 5'phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other PARP2 homology model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 12 % v/v Polypropylene glycol 400
0.1 M Na-acetate
3 % 2 propanol
Crystal Properties Matthews coefficient Solvent content 2.99 58.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.16 α = 90 b = 84.36 β = 90 c = 95.96 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 PIXEL DECTRIS PILATUS3 6M 2016-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.8 30 99.8 0.01 0.0212 1 11.36 4.77 13124
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.93 1.797 0.4
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 PARP2 homology model 2.8 30 12468 657 99.75 0.21127 0.20811 0.2139 0.27392 0.2733 RANDOM 83.666
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] 1.65 -1.22 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_4_deg 24.767 r_dihedral_angle_3_deg 19.227 r_long_range_B_refined 13.73 r_long_range_B_other 13.728 r_scangle_other 10.974 r_mcangle_it 9.822 r_mcangle_other 9.818 r_dihedral_angle_1_deg 7.76 r_scbond_it 7.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.643 r_dihedral_angle_4_deg 24.767 r_dihedral_angle_3_deg 19.227 r_long_range_B_refined 13.73 r_long_range_B_other 13.728 r_scangle_other 10.974 r_mcangle_it 9.822 r_mcangle_other 9.818 r_dihedral_angle_1_deg 7.76 r_scbond_it 7.343 r_scbond_other 7.341 r_mcbond_other 6.494 r_mcbond_it 6.493 r_angle_refined_deg 1.6 r_angle_other_deg 1.201 r_chiral_restr 0.089 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 1849 Nucleic Acid Atoms 824 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing