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Binary complex of DNA Polymerase Beta with Fapy-dG in the template position
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ISB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 14-19% PEG 3350, 50 mM Imidazole pH 8.0, 350 mM Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 2.35 47.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.061 α = 90 b = 78.79 β = 105.66 c = 54.682 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 CMOS RDI CMOS_8M 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.00 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.71 43.78 96.9 0.997 12.6 3.3 45981 21.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.71 9.05 0.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ISB 1.71 43.78 1.34 45981 2204 96.34 0.1938 0.1916 0.1928 0.2364 0.237 27.45
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.0901 f_angle_d 1.3713 f_chiral_restr 0.2957 f_bond_d 0.0119 f_plane_restr 0.0075
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2589 Nucleic Acid Atoms 633 Solvent Atoms 466 Heterogen Atoms
Software Software Software Name Purpose PHENIX phasing PHENIX refinement XDS data reduction XDS data scaling Blu-Ice data collection