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Structure of ARTD2/PARP2 WGR domain bound to double strand DNA without 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 4.9 277 PEG MME 5000
0.1 M Na-acetate
ethylene glyco
Crystal Properties Matthews coefficient Solvent content 3.56 65.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.27 α = 90 b = 119.27 β = 90 c = 73.58 γ = 120
Symmetry Space Group P 63 2 2
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 PILATUS 6M-F 2016-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 Diamond I04
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 2.2 30 99.9 0.08 0.085 1 19.19 9.71 16127 1.46
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.4 99.7 1.557 1.55 0.69 1.6 10
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 2.2 19.98 15320 807 99.66 0.21573 0.21398 0.222 0.2498 0.2548 RANDOM 60.313
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] 0.19 0.1 0.19 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.204 r_dihedral_angle_3_deg 15.662 r_dihedral_angle_4_deg 9.65 r_dihedral_angle_1_deg 6.008 r_long_range_B_refined 5.388 r_long_range_B_other 5.386 r_scangle_other 3.04 r_mcangle_it 2.295 r_mcangle_other 2.294 r_scbond_it 1.834
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.204 r_dihedral_angle_3_deg 15.662 r_dihedral_angle_4_deg 9.65 r_dihedral_angle_1_deg 6.008 r_long_range_B_refined 5.388 r_long_range_B_other 5.386 r_scangle_other 3.04 r_mcangle_it 2.295 r_mcangle_other 2.294 r_scbond_it 1.834 r_scbond_other 1.825 r_angle_refined_deg 1.48 r_mcbond_it 1.348 r_mcbond_other 1.347 r_angle_other_deg 1.154 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 977 Nucleic Acid Atoms 407 Solvent Atoms 39 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing