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Crystal structure of dengue virus type 1 envelope protein in the postfusion conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OK8 PDB entry 1OK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 12.5% PEG 550 MME, 0.1 M MES pH 6.5, 10 mM ZnSO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.78 55.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.65 α = 90 b = 75.65 β = 90 c = 292.802 γ = 120
Symmetry Space Group P 63 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 CCD ADSC QUANTUM 315 Kohzu HLD*-24 monchromator followed by vertical and horizontal focusing mirrors 2007-07-20 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator 2007-08-25 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 APS 24-ID-C 2 SYNCHROTRON NSLS BEAMLINE X25 0.97949 NSLS X25
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 3.5 50 98.7 0.223 12.1 6794 6794 73.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 3.5 3.63 92 0.783 1.64 7.1 607
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT PDB entry 1OK8 3.5 25 6786 6786 311 98.32 0.212 0.208 0.2074 0.297 0.3025 RANDOM 63.849
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] -4.11 -2.06 -4.11 6.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.066 r_dihedral_angle_3_deg 26.037 r_dihedral_angle_4_deg 16.424 r_scangle_it 13.366 r_mcangle_it 11.621 r_dihedral_angle_1_deg 9.401 r_scbond_it 8.8 r_mcbond_it 7.201 r_angle_refined_deg 1.688 r_chiral_restr 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.066 r_dihedral_angle_3_deg 26.037 r_dihedral_angle_4_deg 16.424 r_scangle_it 13.366 r_mcangle_it 11.621 r_dihedral_angle_1_deg 9.401 r_scbond_it 8.8 r_mcbond_it 7.201 r_angle_refined_deg 1.688 r_chiral_restr 0.114 r_bond_refined_d 0.018 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2905 Nucleic Acid Atoms Solvent Atoms 1 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling