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Crystal structure of human polymerase eta with incoming dCMPnPP nucleotide across threofuranosyl thymidine in DNA template at extension stage
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8UJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 0.1M MES pH 5.6, 5mM magnesium chloride, 20% PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.902 α = 90 b = 98.902 β = 90 c = 81.54 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 100 CCD MAR CCD 300 mm 2022-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rpim I (All) 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 2.09 50 98.5 0.1 0.049 0.998 19.3 5.1 26703 22.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.18 70.8 0.494 0.287 0.72 2.34 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.09 36.81 1.38 26638 1279 99.67 0.16 0.1576 0.1579 0.2065 0.2067
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 19.556 f_angle_d 0.905 f_chiral_restr 0.05 f_plane_restr 0.008 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms 388 Solvent Atoms 309 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing Coot model building