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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% polyethylene glycol 8000.
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21 α = 105.662 b = 26.22 β = 96.645 c = 38.64 γ = 91.857
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 1.523 37 87.3 0.164 0.194 0.985 4.44 2.9 10577
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 1.523 1.61 1.526 1.795 0.487
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 1.523 36.893 10562 554 87.615 0.215 0.2117 0.2216 0.281 0.2748 21.771
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] -0.307 0.953 -0.285 1.392 -0.12 -0.84
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.832 r_lrange_other 6.004 r_angle_other_deg 2.357 r_scangle_it 1.894 r_scangle_other 1.894 r_angle_refined_deg 1.599 r_scbond_it 1.361 r_scbond_other 1.361 r_symmetry_nbd_other 0.278 r_xyhbond_nbd_refined 0.259
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 6.832 r_lrange_other 6.004 r_angle_other_deg 2.357 r_scangle_it 1.894 r_scangle_other 1.894 r_angle_refined_deg 1.599 r_scbond_it 1.361 r_scbond_other 1.361 r_symmetry_nbd_other 0.278 r_xyhbond_nbd_refined 0.259 r_nbtor_refined 0.251 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_other 0.226 r_nbd_refined 0.206 r_symmetry_xyhbond_nbd_other 0.186 r_metal_ion_refined 0.158 r_symmetry_nbd_refined 0.145 r_symmetry_nbtor_other 0.096 r_chiral_restr 0.089 r_gen_planes_refined 0.015 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 186 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing