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Crystal structure of full-length NS5 from dengue virus type 3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P97 PDB entries 3P97 and 4HHJ experimental model PDB 4HHJ PDB entries 3P97 and 4HHJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 1.0 M succinic acid (pH 7.0), 0.1 M HEPES (pH 7.0), 1% PEG monomethylether 2000
Crystal Properties Matthews coefficient Solvent content 3.88 68.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 215.314 α = 90 b = 215.314 β = 90 c = 480.683 γ = 120
Symmetry Space Group P 32 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 IMAGE PLATE MAR scanner 300 mm plate 2014-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.978720 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 3.6 50 100 0.33 0.339 0.097 4.6 16.4 149778 100.57
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.66 100 0.866 0.157 6.2 7392
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entries 3P97 and 4HHJ 3.6 49.217 1.34 149621 2004 99.95 0.2386 0.2381 0.2582 0.2737 0.2828 Random selection
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 f_dihedral_angle_d 9.727 f_angle_d 0.478 f_chiral_restr 0.021 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 52457 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 224
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building HKL-2000 data reduction