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The RNA-dependent RNA polymerase domain of dengue 2 NS5, bound with RK-0404678
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J7U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.6 M ammonium sulfate, 100 mM MES-NaOH (pH 6.2-6.5), and 10 mM CoCl2
Crystal Properties Matthews coefficient Solvent content 3.65 66.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 236.5 α = 90 b = 236.5 β = 90 c = 236.5 γ = 90
Symmetry Space Group I 4 3 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 MARMOSAIC 225 mm CCD 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.43 77.2 100 0.205 0.998 16.36 22.3 42503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.43 2.49 2.2895 0.601
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2J7U 2.43 55.744 1.34 42496 2125 99.98 0.1984 0.1967 0.2032 0.2306 0.2377 50.5695
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 5.004 f_angle_d 0.899 f_chiral_restr 0.05 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4730 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 39
Software Software Software Name Purpose xia2 data scaling PHENIX refinement Coot model building xia2 data reduction PHENIX phasing