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Crystal structure analysis of dengue-1 envelope protein domain III
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OAN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 0.1M IMIDAZOLE, 0.2M LITHIUM SULFATE, 30% PEG 3000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 5.076 75.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.087 α = 90 b = 88.087 β = 90 c = 88.087 γ = 90
Symmetry Space Group P 21 3
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 NOIR-1 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.239 ALS 4.2.2
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 2.2 35.97 99.3 0.039 0.038 17.7 3.8 10458
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 98.5 0.694 0.627 1.92 3.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OAN 2.25 35.97 10458 520 99.09 0.21193 0.21145 0.22144 0.2421 RANDOM 32.821
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 37.329 r_dihedral_angle_2_deg 34.602 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 7.326 r_scangle_it 7.116 r_scbond_it 4.677 r_mcangle_it 2.911 r_angle_refined_deg 1.81 r_mcbond_it 1.779 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 37.329 r_dihedral_angle_2_deg 34.602 r_dihedral_angle_3_deg 14.445 r_dihedral_angle_1_deg 7.326 r_scangle_it 7.116 r_scbond_it 4.677 r_mcangle_it 2.911 r_angle_refined_deg 1.81 r_mcbond_it 1.779 r_chiral_restr 0.094 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 787 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction