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Racemic compound of RNA duplexes.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ZQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M zinc acetate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.189 α = 105.791 b = 26.592 β = 97.082 c = 38.969 γ = 91.17
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 PILATUS 6M 2019-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.283 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 1.6 36.2 85.7 0.089 0.126 0.99 5.17 1.9 18361
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 0.51 0.722 0.889 1.32
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 6ZQ9 1.601 36.2 9717 510 90.856 0.193 0.191 0.1982 0.2278 0.243 18.289
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] -0.027 0.404 0.084 1.053 -0.184 -0.798
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.893 r_lrange_other 4.185 r_scangle_it 2.007 r_scangle_other 2.006 r_angle_refined_deg 1.644 r_scbond_it 1.449 r_scbond_other 1.449 r_angle_other_deg 1.187 r_metal_ion_refined 0.282 r_symmetry_nbd_other 0.27
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.893 r_lrange_other 4.185 r_scangle_it 2.007 r_scangle_other 2.006 r_angle_refined_deg 1.644 r_scbond_it 1.449 r_scbond_other 1.449 r_angle_other_deg 1.187 r_metal_ion_refined 0.282 r_symmetry_nbd_other 0.27 r_xyhbond_nbd_refined 0.266 r_nbtor_refined 0.252 r_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.193 r_nbd_other 0.189 r_symmetry_nbd_refined 0.162 r_chiral_restr 0.064 r_symmetry_nbtor_other 0.064 r_symmetry_xyhbond_nbd_other 0.021 r_gen_planes_refined 0.02 r_bond_refined_d 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 676 Solvent Atoms 146 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing