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Crystal structure of human DNA polymerase eta incorporating ITP across dT
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 2.12 41.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.9 α = 90 b = 98.9 β = 90 c = 81.222 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 120 PIXEL DECTRIS EIGER X 9M 2022-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97933 NSLS-II 17-ID-1
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 1.737 58.936 86 0.9994 15.35 11.96 39730 28.43
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 1.737 1.768 0.4548 1.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB entry 4O3N 1.74 42.82 1.34 39698 1976 85.24 0.2132 0.2114 0.2452 0.2517 36.66
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 19.9733 f_angle_d 1.1764 f_chiral_restr 0.0798 f_plane_restr 0.01 f_bond_d 0.0092
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3337 Nucleic Acid Atoms 386 Solvent Atoms 167 Heterogen Atoms 32
Software Software Software Name Purpose Coot model building PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing