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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 41.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.109 α = 105.858 b = 26.722 β = 97.598 c = 38.971 γ = 90.857
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 1.7 37 88 0.1 0.142 0.986 5.1 1.9 15768
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 1.7 1.8 0.35 0.496 0.884 2.02
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 1.7 37 8271 423 92.506 0.191 0.1884 0.197 0.2479 0.2594 14.819
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] -0.06 1.067 -0.813 1.12 -0.653 -0.398
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.593 r_lrange_other 3.702 r_angle_other_deg 2.424 r_angle_refined_deg 1.638 r_scangle_it 1.336 r_scangle_other 1.335 r_scbond_other 0.947 r_scbond_it 0.946 r_xyhbond_nbd_refined 0.286 r_symmetry_nbd_other 0.269
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.593 r_lrange_other 3.702 r_angle_other_deg 2.424 r_angle_refined_deg 1.638 r_scangle_it 1.336 r_scangle_other 1.335 r_scbond_other 0.947 r_scbond_it 0.946 r_xyhbond_nbd_refined 0.286 r_symmetry_nbd_other 0.269 r_nbtor_refined 0.249 r_nbd_refined 0.215 r_symmetry_xyhbond_nbd_refined 0.207 r_nbd_other 0.19 r_metal_ion_refined 0.179 r_symmetry_nbd_refined 0.148 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.088 r_symmetry_xyhbond_nbd_other 0.038 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 162 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing