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X-ray structure of human ABH2 bound to dsDNA through active site cross-linking
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 8% PEG 8000, 0.1M sodium chloride, 0.05M magnesium chloride, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.14 α = 90 b = 78.14 β = 90 c = 229.59 γ = 120
Symmetry Space Group P 65 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9266 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 98.8 0.035 44.5 9.7 28880 28880
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 91.9 0.398 2.7 5.7 2606
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2 20 26213 1423 95.4 0.21974 0.21927 0.2106 0.22797 0.2151 RANDOM 43.73
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] -0.28 -0.14 -0.28 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.241 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 5.485 r_scangle_it 1.624 r_angle_refined_deg 1.206 r_scbond_it 1.004 r_mcangle_it 0.669 r_mcbond_it 0.384 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.241 r_dihedral_angle_4_deg 15.157 r_dihedral_angle_3_deg 12.988 r_dihedral_angle_1_deg 5.485 r_scangle_it 1.624 r_angle_refined_deg 1.206 r_scbond_it 1.004 r_mcangle_it 0.669 r_mcbond_it 0.384 r_nbtor_refined 0.295 r_symmetry_hbond_refined 0.19 r_nbd_refined 0.171 r_symmetry_vdw_refined 0.156 r_xyhbond_nbd_refined 0.121 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_refined 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 1636 Nucleic Acid Atoms 527 Solvent Atoms 192 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing