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RNA polymerase II elongation complex with 8-oxoG in syn-conformation with added AMP
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 298 390mM (NH4)2HPO4/NaH2PO4, pH 6.5, 5mM dioxane, 5mM DTT, 10-12% PEG6000
Crystal Properties Matthews coefficient Solvent content 3.68 66.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.54 α = 90 b = 223.101 β = 100.38 c = 195.002 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 2019-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.9999 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 3.6 49.22 99.9 0.559 0.6 0.216 0.984 4.4 7.6 81363
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 3.6 3.67 99.7 8.839 9.478 3.413 0.236 7.7
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 49.22 1.33 79423 1998 97.56 0.2487 0.2478 0.2486 0.2807 0.2805
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 17.848 f_angle_d 0.627 f_chiral_restr 0.042 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27987 Nucleic Acid Atoms 1059 Solvent Atoms Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHENIX phasing