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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 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.094 α = 106.555 b = 26.974 β = 96.898 c = 38.844 γ = 91.6
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 36.9 85.4 0.072 0.102 0.994 6 1.9 18254
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 0.472 0.668 0.866 1.21
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 1.602 36.9 9704 481 90.904 0.183 0.1808 0.1881 0.2243 0.2315 18.962
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] 0.158 0.661 -0.075 0.565 -0.071 -0.571
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.01 r_lrange_other 4.477 r_angle_other_deg 2.387 r_scangle_it 1.957 r_scangle_other 1.956 r_angle_refined_deg 1.646 r_scbond_it 1.414 r_scbond_other 1.414 r_symmetry_nbd_other 0.261 r_nbtor_refined 0.252
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.01 r_lrange_other 4.477 r_angle_other_deg 2.387 r_scangle_it 1.957 r_scangle_other 1.956 r_angle_refined_deg 1.646 r_scbond_it 1.414 r_scbond_other 1.414 r_symmetry_nbd_other 0.261 r_nbtor_refined 0.252 r_xyhbond_nbd_refined 0.243 r_nbd_refined 0.22 r_symmetry_xyhbond_nbd_refined 0.188 r_nbd_other 0.178 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.087 r_symmetry_nbd_refined 0.086 r_metal_ion_refined 0.064 r_gen_planes_refined 0.02 r_bond_refined_d 0.009 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 164 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing