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RNA-imidazolium-bridged dinucleotide intermediate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6C8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 10% w/v Polyethylene glycol 6,000, 0.05 M HEPES pH 7.0, 0.2 M Ammonium acetate, 0.15 M Magnesium acetate
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.592 α = 90 b = 49.592 β = 90 c = 81.941 γ = 120
Symmetry Space Group P 3 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 99 PIXEL DECTRIS EIGER X 16M 2021-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.033175 APS 23-ID-B
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 1.528 50 96.9 0.079 0.087 0.035 0.979 15.9 5.9 17783
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 1.528 1.56 84.9 0.419 0.464 0.203 0.86 2.8 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.528 42.948 17651 889 96.448 0.2 0.1984 0.2035 0.2345 0.2411 15.946
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] -0.001
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.846 r_lrange_other 5.125 r_angle_other_deg 3.607 r_scangle_it 3.49 r_scangle_other 3.488 r_angle_refined_deg 3.041 r_scbond_it 2.277 r_scbond_other 2.276 r_chiral_restr_other 1.82 r_chiral_restr 0.48
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.846 r_lrange_other 5.125 r_angle_other_deg 3.607 r_scangle_it 3.49 r_scangle_other 3.488 r_angle_refined_deg 3.041 r_scbond_it 2.277 r_scbond_other 2.276 r_chiral_restr_other 1.82 r_chiral_restr 0.48 r_symmetry_nbtor_other 0.246 r_nbtor_refined 0.244 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.162 r_nbd_other 0.153 r_symmetry_xyhbond_nbd_refined 0.138 r_dihedral_angle_other_2_deg 0.089 r_symmetry_nbd_refined 0.079 r_nbd_refined 0.075 r_bond_other_d 0.027 r_bond_refined_d 0.021 r_gen_planes_refined 0.02 r_metal_ion_refined 0.012 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 598 Solvent Atoms 201 Heterogen Atoms 111
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing