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Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the super-open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UM3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 ul of 0.3 mM protein and 0.4 mM of the compound NSC83614 in 100 mM NaCl, 20 mM Tris-Cl buffer (pH 8.0), was mixed with 0.2 ul of the well solution.
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.81 α = 98.88 b = 42.637 β = 92.11 c = 46.296 γ = 90.41
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 12M 2020-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 1.19499 SSRL BL14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.6 33.68 93.9 0.023 0.029 0.996 25.1 2.6 38226
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 72.9 0.076 0.992 8.2 2.2
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-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 6um3 1.6 33.68 36353 1872 93.95 0.15975 0.1731 0.189 0.1964 THROUGHOUT RANDOM 28.72
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 19.6702 f_angle_d 1.8412 f_chiral_restr 0.1117 f_bond_d 0.0155 f_plane_restr 0.0118
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2490 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing