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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 polyehtylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 2.03 39.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.095 α = 104.6 b = 25.955 β = 96.804 c = 38.514 γ = 91.765
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 2.455 36.9 82.2 0.121 0.171 0.978 4.09 1.87 4734
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 2.455 2.6 61.4 0.352 0.497 0.836
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 2.455 36.7 2519 121 87.739 0.183 0.1779 0.1863 0.2837 0.2953 29.174
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] -3.158 0.809 -0.006 5.444 0.232 -2.102
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.284 r_lrange_other 5.518 r_scangle_it 3.348 r_scangle_other 3.347 r_scbond_it 2.186 r_scbond_other 2.184 r_angle_refined_deg 1.668 r_angle_other_deg 1.248 r_metal_ion_refined 0.386 r_xyhbond_nbd_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.284 r_lrange_other 5.518 r_scangle_it 3.348 r_scangle_other 3.347 r_scbond_it 2.186 r_scbond_other 2.184 r_angle_refined_deg 1.668 r_angle_other_deg 1.248 r_metal_ion_refined 0.386 r_xyhbond_nbd_refined 0.293 r_symmetry_nbd_other 0.283 r_nbtor_refined 0.253 r_nbd_other 0.225 r_symmetry_xyhbond_nbd_refined 0.181 r_nbd_refined 0.164 r_symmetry_nbd_refined 0.139 r_symmetry_xyhbond_nbd_other 0.122 r_chiral_restr 0.068 r_symmetry_nbtor_other 0.062 r_gen_planes_refined 0.011 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 81 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing