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Unliganded structure of RNA duplex containing UGGAA/UGGAA motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9I9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 292 0.012M Sodium chloride, 0.08M Potassium chloride, 0.04M Sodium cacodylate trihydrate pH 5.5 45% v/v (+/-)-2-Methyl-2,4-pentanediol, 0.002M Hexammine cobalt(III) chloride
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.818 α = 90 b = 33.818 β = 90 c = 170.094 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 4M 2023-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.79 42.52 97.3 0.999 16.72 6.26 2764
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 2.96 0.982
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.79 42.52 2762 277 97.254 0.262 0.2573 0.2608 0.3085 0.3124 28.256
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] 3.992 3.992 -7.984
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.742 r_angle_other_deg 1.587 r_symmetry_xyhbond_nbd_refined 0.376 r_nbtor_refined 0.252 r_symmetry_nbd_other 0.249 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.206 r_nbd_refined 0.163 r_symmetry_nbd_refined 0.152 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_angle_refined_deg 1.742 r_angle_other_deg 1.587 r_symmetry_xyhbond_nbd_refined 0.376 r_nbtor_refined 0.252 r_symmetry_nbd_other 0.249 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.206 r_nbd_refined 0.163 r_symmetry_nbd_refined 0.152 r_chiral_restr 0.104 r_symmetry_nbtor_other 0.072 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_lrange_it r_lrange_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 642 Solvent Atoms 6 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing