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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 aceate, 0.1 M cacodylate buffer, 18% w/v polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.04 39.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 21.13 α = 106.094 b = 26.76 β = 97.185 c = 38.82 γ = 91.419
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 1.528 37 89.2 0.086 0.096 0.997 9.4 5.3 10955
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 1.528 1.62 74.7 0.557 0.618 0.946 2.03 5.1
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 1.528 36.945 10942 567 89.22 0.205 0.2027 0.2109 0.2527 0.2543 18.513
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] 0.224 0.384 -0.076 1.073 -0.486 -0.832
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.562 r_lrange_other 3.935 r_angle_other_deg 2.37 r_scangle_it 2.047 r_scangle_other 2.046 r_angle_refined_deg 1.737 r_scbond_it 1.561 r_scbond_other 1.56 r_xyhbond_nbd_refined 0.294 r_symmetry_nbd_other 0.271
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 4.562 r_lrange_other 3.935 r_angle_other_deg 2.37 r_scangle_it 2.047 r_scangle_other 2.046 r_angle_refined_deg 1.737 r_scbond_it 1.561 r_scbond_other 1.56 r_xyhbond_nbd_refined 0.294 r_symmetry_nbd_other 0.271 r_symmetry_xyhbond_nbd_refined 0.255 r_nbtor_refined 0.248 r_nbd_other 0.206 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_other 0.192 r_metal_ion_refined 0.183 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.091 r_gen_planes_refined 0.02 r_bond_refined_d 0.01 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 166 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing