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RNA polymerase II elongation complex with Fapy-dG lesion soaking with CTP before chemistry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 390 mM ammonium phosphate (pH 6.0), 5 mM DTT, 5 mM dioxane, and 9-13% (w/v) PEG 6,000
Crystal Properties Matthews coefficient Solvent content 3.37 63.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.118 α = 90 b = 221.626 β = 97.4 c = 189.961 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS3 2M 2023-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9774 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.39 47.76 99.9 0.524 0.566 0.214 0.984 4.6 6.9 89064
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.39 3.45 99.2 4.497 4.874 1.858 0.35 6.8
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 3.4 47.76 1.33 87375 1998 98.91 0.2675 0.2667 0.2667 0.3015 0.3016
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 13.477 f_angle_d 0.831 f_chiral_restr 0.048 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28013 Nucleic Acid Atoms 950 Solvent Atoms Heterogen Atoms 39
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing