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Crystal structure of human DNA polymerase eta incorporating 5F-dUTP across dA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4O3N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100 mM MES, pH 6.5, 20% PEG2000 MME, 5 mM calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.907 α = 90 b = 97.907 β = 90 c = 81.008 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 PIXEL DECTRIS EIGER X 16M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97934 NSLS-II 17-ID-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 2.784 58.573 94 0.9944 7.3 13.14 10380 55.58
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 2.784 2.837 0.4833 1.31
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 PDB entry 4O3N 2.784 48.95 1.33 10363 461 92.88 0.2036 0.1997 0.2015 0.2815 0.2798 53.97
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 19.9559 f_angle_d 1.1403 f_chiral_restr 0.0541 f_bond_d 0.0101 f_plane_restr 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3326 Nucleic Acid Atoms 387 Solvent Atoms 5 Heterogen Atoms 61
Software Software Software Name Purpose autoPROC data processing PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing