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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/ polyeth7ylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 2.08 40.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.193 α = 105.044 b = 26.339 β = 97.539 c = 38.928 γ = 91.127
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 2.29 37.2 85.7 0.133 0.189 0.972 3.87 1.9 6237
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 2.29 2.43 0.474 0.67 0.631 1.38
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 2.29 37.2 3286 178 90.573 0.175 0.1691 0.1752 0.2742 0.2817 23.557
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] -0.4 1.198 -0.666 2.606 -0.111 -1.685
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.143 r_lrange_other 4.725 r_scangle_it 2.735 r_scangle_other 2.734 r_angle_other_deg 2.269 r_scbond_other 1.776 r_scbond_it 1.774 r_angle_refined_deg 1.707 r_xyhbond_nbd_refined 0.29 r_symmetry_nbd_other 0.284
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.143 r_lrange_other 4.725 r_scangle_it 2.735 r_scangle_other 2.734 r_angle_other_deg 2.269 r_scbond_other 1.776 r_scbond_it 1.774 r_angle_refined_deg 1.707 r_xyhbond_nbd_refined 0.29 r_symmetry_nbd_other 0.284 r_nbtor_refined 0.256 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_other 0.204 r_nbd_refined 0.191 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.095 r_metal_ion_refined 0.091 r_symmetry_xyhbond_nbd_other 0.059 r_symmetry_nbd_refined 0.049 r_gen_planes_refined 0.015 r_bond_refined_d 0.008 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 98 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing