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Crystal structure of the full-length Zika virus NS5 protein (Human isolate Z1106033)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M2X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 100 mM Sodium Acetate, 1 M di-potassium hydrogen phosphate, 0.95 M sodium di-hydrogen phosphate.
Crystal Properties Matthews coefficient Solvent content 5.15 76.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 234.578 α = 90 b = 234.578 β = 90 c = 406.123 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 100 PIXEL DECTRIS PILATUS 6M 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97928 ALBA XALOC
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 4.8 44.07 99.7 0.159 5.9 3.3 61390
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 4.8 5.06 99.4 1.495 3.1
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 FREE R-VALUE 5m2x 4.8 44.323 1.33 61148 3118 99.38 0.2419 0.2407 0.2574 0.2657 0.2816
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 19.219 f_angle_d 0.53 f_chiral_restr 0.039 f_plane_restr 0.004 f_bond_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 42582 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 174
Software Software Software Name Purpose PHENIX refinement XDS data reduction SCALA data scaling MOLREP phasing