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Crystal structure of the complete turnip yellow mosaic virus 3'UTR
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4P5J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 5 mg/mL RNA was resuspended in 2.5 mM magnesium chloride and 10 mM HEPES KOH pH 7.4 and DPEC treated water. The RNA was heated at 65 degrees Celsius and slow cooled to room temperature followed by the addition of spermidine (0.5 mM final). Crystals were grown in 50 mM cacodylate, 2.5 M ammonium sulfate, 20 mM magnesium chloride, 1.0 mM spermine, and 2 mM hexamine cobalt chloride
Crystal Properties Matthews coefficient Solvent content 4.29 71.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.032 α = 90 b = 129.126 β = 90 c = 172.005 γ = 90
Symmetry Space Group I 2 2 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 CMOS RDI CMOS_8M 2017-05-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.072 ALS 4.2.2
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 3.1 35.79 89.41 0.088 0.095 0.036 0.999 16.69 7.1 21141
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.2 64.37 1.69 1.83 0.69 1.37 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4p5j 3.1 35.79 1.35 18974 1629 89.49 0.2303 0.2269 0.2346 0.2662 0.2758
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 15.716 f_angle_d 1.517 f_chiral_restr 0.059 f_plane_restr 0.01 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 4286 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHENIX phasing