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Crystal structure of DEN4 ED3 mutant with epitope two residues substituted from DEN3 ED3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WE1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 PEG 3350, Ammonium sulphate, Tris-HCL, Dioxane
Crystal Properties Matthews coefficient Solvent content 2.79 55.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.585 α = 90 b = 124.585 β = 90 c = 86.132 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 270 2014-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9800 Photon Factory BL-17A
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 2.78 50 100 0.135 37.8 13.6 19294
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 2.78 2.83 100 0.872 5 12.9
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 3WE1 2.78 40.03 18330 938 99.78 0.23584 0.23392 0.2338 0.27277 0.2704 RANDOM 53.644
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] 0.1 0.1 0.1 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 15.312 r_dihedral_angle_1_deg 6.239 r_angle_other_deg 1.538 r_angle_refined_deg 1.512 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 21.886 r_dihedral_angle_3_deg 15.312 r_dihedral_angle_1_deg 6.239 r_angle_other_deg 1.538 r_angle_refined_deg 1.512 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.007 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4544 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data processing MOLREP phasing