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T7 RNA polymerase elongation complex with unnatural base dDs-PaTP pair
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8DH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 298 10% PEG 8000, 8% glycerol, 5 mM B-mercaptoethanol, 100 mM Tris pH 8.1
Crystal Properties Matthews coefficient Solvent content 2.89 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.866 α = 89.85 b = 86.156 β = 85.09 c = 201.676 γ = 69.56
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 EIGER X 16M 2021-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 1 SSRL BL12-1
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 2.65 39.34 90.3 0.121 0.14 0.071 0.994 8.1 3.9 130161
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 2.65 2.69 89.9 2.619 3.036 1.533 0.315 3.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8DH0 2.65 39.34 1.96 128924 6387 89.58 0.2318 0.2297 0.2306 0.2715 0.2711
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 13.774 f_angle_d 0.697 f_chiral_restr 0.045 f_plane_restr 0.009 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24720 Nucleic Acid Atoms 2302 Solvent Atoms 63 Heterogen Atoms 2
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction PHENIX phasing