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DengueV-2 Capsid Structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VG5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 291 3.0 M NaNO3, 100 mM HEPES pH 7.2, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 3.49 64.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142 α = 90 b = 142 β = 90 c = 67 γ = 120
Symmetry Space Group P 31 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 CCD RAYONIX MX300-HS Be lenses 2018-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 50 100 0.132 0.139 0.042 5 11.1 15870
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 3 3.05 100 0.926 0.97 0.29 0.939 2.83 11.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VG5 3.001 45.302 1.35 14348 1442 90.78 0.1896 0.1858 0.1896 0.2246 0.2267 Random 55.3994
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3592 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 98
Software Software Software Name Purpose PHENIX refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction