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Structure of ARTD2/PARP2 WGR domain bound to double strand DNA with 5 nucleotide overhang and 5'phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6F1K PDB ID 6F1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Na-formate
20 % PEG 3350
20 % glycerol
Crystal Properties Matthews coefficient Solvent content 3.46 64.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.15 α = 90 b = 87.15 β = 90 c = 185.27 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 PILATUS 6M-F 2016-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 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 2.98 20 99.8 0.069 0.075 0.88 15.29 6.38 23275
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3
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 PDB ID 6F1K 2.98 19.86 21936 1155 99.21 0.23056 0.22822 0.233 0.2753 0.273 RANDOM 121.612
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] 3.9 7.42 -11.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.531 r_dihedral_angle_3_deg 18.868 r_long_range_B_refined 16.965 r_long_range_B_other 16.964 r_dihedral_angle_4_deg 15.417 r_scangle_other 14.351 r_mcangle_it 13.985 r_mcangle_other 13.982 r_scbond_it 9.755 r_scbond_other 9.755
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.531 r_dihedral_angle_3_deg 18.868 r_long_range_B_refined 16.965 r_long_range_B_other 16.964 r_dihedral_angle_4_deg 15.417 r_scangle_other 14.351 r_mcangle_it 13.985 r_mcangle_other 13.982 r_scbond_it 9.755 r_scbond_other 9.755 r_mcbond_it 9.41 r_mcbond_other 9.401 r_dihedral_angle_1_deg 6.826 r_angle_refined_deg 1.778 r_angle_other_deg 1.178 r_chiral_restr 0.115 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 3780 Nucleic Acid Atoms 1232 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing