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Crystal structure of the dengue 2 virus envelope glycoprotein in the postfusion conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAM PDB ENTRY 1OAM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20-30% PEG 400, 0.08 M NACL, 0.1 M MOPS PH 7-8.
Crystal Properties Matthews coefficient Solvent content 2.445 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.151 α = 90 b = 76.151 β = 90 c = 130.775 γ = 120
Symmetry Space Group P 3 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 ADSC CCD 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C APS 14-BM-C
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 50 95 0.058 25 7 28677 11.3
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 2.07 75 0.398 2 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1OAM 2 29.29 27450 1322 91 0.222 0.222 0.2219 0.267 0.2662 RANDOM 30.1
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] 1.49 2.18 1.49 -2.98
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.4 c_scangle_it 6.41 c_scbond_it 4.76 c_mcangle_it 4.22 c_mcbond_it 3.29 c_angle_deg 1.4 c_improper_angle_d 0.82 c_bond_d 0.006 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.4 c_scangle_it 6.41 c_scbond_it 4.76 c_mcangle_it 4.22 c_mcbond_it 3.29 c_angle_deg 1.4 c_improper_angle_d 0.82 c_bond_d 0.006 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2962 Nucleic Acid Atoms Solvent Atoms 205 Heterogen Atoms 15
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing CNS phasing CNS refinement