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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 38.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.95 α = 106.033 b = 26.49 β = 96.057 c = 38.66 γ = 92.598
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 2018-12-01 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 1.52 37 86.7 0.168 0.198 0.975 4.19 3.5 10572
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 1.52 1.61 1.061 1.252 0.652
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 1.522 36.874 10553 563 86.756 0.216 0.2128 0.2198 0.2721 0.2735 20.915
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] -0.731 0.709 0.242 1.541 0.039 -0.802
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.742 r_lrange_other 5.432 r_scangle_it 1.873 r_scangle_other 1.872 r_angle_refined_deg 1.436 r_scbond_it 1.304 r_scbond_other 1.303 r_angle_other_deg 1.182 r_symmetry_xyhbond_nbd_other 0.318 r_symmetry_nbd_other 0.272
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.742 r_lrange_other 5.432 r_scangle_it 1.873 r_scangle_other 1.872 r_angle_refined_deg 1.436 r_scbond_it 1.304 r_scbond_other 1.303 r_angle_other_deg 1.182 r_symmetry_xyhbond_nbd_other 0.318 r_symmetry_nbd_other 0.272 r_xyhbond_nbd_refined 0.268 r_nbtor_refined 0.253 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.215 r_nbd_other 0.169 r_symmetry_nbd_refined 0.131 r_metal_ion_refined 0.081 r_chiral_restr 0.062 r_symmetry_nbtor_other 0.062 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 187 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing