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Crystal structure of Dengue 4 Envelope protein domain III (ED3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AUJ PDB ENTRY 3AUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 30.0% PEG 3350, 0.2M Ammonium sulphate, 0.1M Tris-HCl pH 8.5, 1% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.32 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.38 α = 90 b = 91.38 β = 90 c = 73.109 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 195 CCD ADSC QUANTUM 315r Mono-chromator 17.5 m
Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling
Vertical Focusing Mirror 22.22 m
Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 100 mm (W) x 50 mm (T) ) with 4.0 mrad glancing angle.
Horizontal Focusing Mirror 29.5 m
Rhodium coated silicon single crystal (Flat shaped, 1000 mm (L) x 100 mm (W) x 40 mm (T) ) with 4.0 mrad glancing angle. 2012-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.27 10 100 0.064 0.2669 29.07 13.6 14490 3 33.8
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3AUJ 2.278 9.967 1.34 14456 732 99.94 0.2669 0.2669 0.2657 0.2947 0.2897 0.3226 37.76
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] -2.9864 -2.9864 5.9728
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 15.063 f_angle_d 1.132 f_chiral_restr 0.069 f_bond_d 0.008 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1461 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building PHENIX refinement DENZO data reduction SCALEPACK data scaling PHENIX phasing