☰ Navigation Tabs
Crystal structure of an exonuclease resistant RNA from Zika virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PQV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 drop: 1 uL 5 mg/mL RNA in 2.5 mM magnesium chloride, 10 mM HEPES-KOH pH 7.5 (heated to 65 C for 3 minutes, cooled at room temperature, 0.5 mM spermidine added, centrifuged for 10 minutes at 13000 x g) + 1 uL 50 mM sodium cacodylate pH 6.0, 150 mM NaCl, 4 mM CaCl2, 0.6 mM spermine, 36% 1,6-hexanediol. Crystals were flash-frozen in the mother liquor using liquid nitrogen for x-ray diffraction.
Crystal Properties Matthews coefficient Solvent content 3.55 65.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.679 α = 90 b = 111.679 β = 90 c = 90.826 γ = 120
Symmetry Space Group P 64 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 2016-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0972 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.805 55.839 99.6 0.092 31.5 21.1 15501
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.81 2.91 99.9 1.492 0.82 2.3 21.1
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 4pqv 2.805 55.839 1.34 15501 1532 99.66 0.1933 0.1906 0.1932 0.2177 0.2228
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 12.49 f_angle_d 1.103 f_chiral_restr 0.045 f_plane_restr 0.007 f_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms Nucleic Acid Atoms 1527 Solvent Atoms 10 Heterogen Atoms 9
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing