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The crystal structure of dG(Se-Rp)-DNA:Pol X product binary complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HRB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 ammonium sulfate (0.2 M), Bis-Tris pH 6.5 (0.1 M), 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.54 51.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.42 α = 90 b = 87.344 β = 91.16 c = 87.48 γ = 90
Symmetry Space Group P 1 21 1
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 325 mm CCD 2020-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 1.9 30 97.1 0.06 9.6 5 69608
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 1.9 1.97 87.4 0.264 3.4
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 30 61518 3219 90.39 0.21657 0.21517 0.2201 0.24293 0.2475 RANDOM 23.102
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] -0.25 -0.25 -0.37 0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.957 r_dihedral_angle_4_deg 15.056 r_dihedral_angle_3_deg 13.267 r_long_range_B_refined 5.232 r_dihedral_angle_1_deg 5.162 r_long_range_B_other 4.516 r_mcangle_it 1.65 r_mcangle_other 1.65 r_scangle_other 1.357 r_angle_refined_deg 1.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.957 r_dihedral_angle_4_deg 15.056 r_dihedral_angle_3_deg 13.267 r_long_range_B_refined 5.232 r_dihedral_angle_1_deg 5.162 r_long_range_B_other 4.516 r_mcangle_it 1.65 r_mcangle_other 1.65 r_scangle_other 1.357 r_angle_refined_deg 1.226 r_angle_other_deg 1.096 r_mcbond_it 0.923 r_mcbond_other 0.923 r_scbond_it 0.788 r_scbond_other 0.782 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 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 5673 Nucleic Acid Atoms 644 Solvent Atoms 711 Heterogen Atoms 48
Software Software Software Name Purpose HKL-3000 data scaling REFMAC refinement HKL-3000 data reduction PHASER phasing