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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 2.02 39.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.066 α = 105.511 b = 25.968 β = 96.328 c = 38.566 γ = 92.161
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 36.9 83.2 0.103 0.146 0.984 4.62 1.9 9111
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 0.407 0.576 0.788 1.63
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 1.98 36.87 4852 260 88.816 0.178 0.1741 0.184 0.25 0.2568 22.093
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] -0.919 0.028 -0.166 1.947 -0.633 -0.527
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.033 r_lrange_other 4.144 r_scangle_it 2.123 r_scangle_other 2.123 r_scbond_it 1.5 r_scbond_other 1.5 r_angle_refined_deg 1.468 r_angle_other_deg 1.256 r_symmetry_nbd_other 0.278 r_xyhbond_nbd_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 5.033 r_lrange_other 4.144 r_scangle_it 2.123 r_scangle_other 2.123 r_scbond_it 1.5 r_scbond_other 1.5 r_angle_refined_deg 1.468 r_angle_other_deg 1.256 r_symmetry_nbd_other 0.278 r_xyhbond_nbd_refined 0.262 r_nbtor_refined 0.252 r_nbd_other 0.206 r_nbd_refined 0.194 r_symmetry_xyhbond_nbd_refined 0.187 r_metal_ion_refined 0.143 r_symmetry_nbd_refined 0.092 r_symmetry_nbtor_other 0.062 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.032 r_gen_planes_refined 0.014 r_bond_refined_d 0.007 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 122 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing