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Crystal structure of an exoribonuclease-resistant RNA from a Tombusvirus-like associated RNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JJU (chain A)res 7, 21-29, 32 (chain B)res 44-49 experimental model PDB 6D3P (chain A)res 7, 18-26, 28 (chain B)res 40-45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 well solution:
0.02 M Magnesium chloride hexahydrate
0.05 M Sodium cacodylate trihydrate pH 7.0
15% v/v 2-Propanol
0.001 M Hexammine cobalt(III) chloride
0.001 M Spermine
5 mg/mL RNA was dissolved in:
2.5 mM MgCl2
10 mM HEPES-KOH pH 7.5
0.5 mM spermidine
300 nL sitting drops were set up using the mosquito with a 1:1 well:RNA ratio
Crystal Properties Matthews coefficient Solvent content 2.46 50.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.637 α = 90 b = 42.392 β = 103.62 c = 84.491 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER2 X 9M 2023-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.979 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.9 41.06 87.25 0.101 0.1177 0.05966 0.981 10.53 3.7 8421 55.77
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.004 58.81 0.8365 0.9738 0.4913 0.817 1.71 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.9 41.06 1.34 7384 739 87.28 0.2214 0.2173 0.2174 0.2581 0.2593 52.6
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.7816 f_angle_d 0.5034 f_chiral_restr 0.0246 f_plane_restr 0.0028 f_bond_d 0.0017
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 2333 Solvent Atoms Heterogen Atoms 170
Software Software Software Name Purpose PHENIX refinement XDS data reduction STARANISO data scaling PHENIX phasing