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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% polyethylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 1.95 36.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.018 α = 104.931 b = 25.804 β = 96.588 c = 38.414 γ = 92.107
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 2019-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.283 BESSY 14.1
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 1.98 37 81.4 0.099 0.14 0.985 4.31 1.9 8769
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 1.98 2.1 69.2 0.479 0.677 0.782
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 1.981 36.809 4678 244 86.984 0.177 0.1725 0.1822 0.2592 0.2713 26.045
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] -0.626 0.925 -0.218 1.807 -0.294 -0.875
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.752 r_lrange_other 4.27 r_scangle_it 2.814 r_scangle_other 2.813 r_angle_other_deg 2.266 r_scbond_other 2.099 r_scbond_it 2.097 r_angle_refined_deg 1.657 r_xyhbond_nbd_refined 0.286 r_symmetry_nbd_other 0.277
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.752 r_lrange_other 4.27 r_scangle_it 2.814 r_scangle_other 2.813 r_angle_other_deg 2.266 r_scbond_other 2.099 r_scbond_it 2.097 r_angle_refined_deg 1.657 r_xyhbond_nbd_refined 0.286 r_symmetry_nbd_other 0.277 r_nbtor_refined 0.254 r_symmetry_xyhbond_nbd_refined 0.231 r_metal_ion_refined 0.218 r_nbd_other 0.21 r_nbd_refined 0.19 r_chiral_restr 0.11 r_symmetry_nbd_refined 0.105 r_symmetry_nbtor_other 0.092 r_symmetry_xyhbond_nbd_other 0.075 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 676 Solvent Atoms 114 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing