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RNA polymerase II elongation complex with Fapy-dG lesion with CMP added
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 3.62 66.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.103 α = 90 b = 224.009 β = 99.98 c = 192.541 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 2023-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97648 ALS 5.0.3
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 3.51 49.24 99.4 0.389 0.42 0.158 0.991 6.1 7 85895
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 3.51 3.57 98.7 4.735 5.14 1.971 0.215 6.7
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 3.6 49.24 1.33 79243 1997 98.9 0.2588 0.2576 0.2592 0.3015 0.3009
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 12.702 f_angle_d 0.779 f_chiral_restr 0.05 f_plane_restr 0.006 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 28002 Nucleic Acid Atoms 971 Solvent Atoms Heterogen Atoms 18
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing