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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 polyehylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2 38.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 20.97 α = 105.839 b = 26.43 β = 96.657 c = 38.68 γ = 92.025
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 Merge 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 88.2 0.069 0.081 0.998 9.49 3.55 10765
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.61 74.1 0.566 0.664 0.889 1.78 3.5
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ZQ9 1.52 36.893 10761 567 88.321 0.19 0.1874 0.2352 0.2489 16.865
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] -0.312 0.435 -0.357 1.633 -0.462 -0.823
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.779 r_lrange_other 3.948 r_angle_refined_deg 1.746 r_scangle_it 1.691 r_scangle_other 1.69 r_scbond_it 1.288 r_scbond_other 1.286 r_angle_other_deg 1.266 r_symmetry_nbd_other 0.277 r_xyhbond_nbd_refined 0.263
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.779 r_lrange_other 3.948 r_angle_refined_deg 1.746 r_scangle_it 1.691 r_scangle_other 1.69 r_scbond_it 1.288 r_scbond_other 1.286 r_angle_other_deg 1.266 r_symmetry_nbd_other 0.277 r_xyhbond_nbd_refined 0.263 r_nbtor_refined 0.247 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.208 r_nbd_other 0.184 r_symmetry_xyhbond_nbd_other 0.174 r_metal_ion_refined 0.155 r_symmetry_nbd_refined 0.142 r_chiral_restr 0.07 r_symmetry_nbtor_other 0.066 r_gen_planes_refined 0.022 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 676 Solvent Atoms 181 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing