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Crystal Structure of Unlinked NS2B_NS3 Protease from Zika Virus in Complex with Inhibitor MI-2223
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GPI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 291 0.1 M sodium acetate
0.2 M ammonium sulfate
19 % PEG2000
macroseeding was performed to obtain larger crystal
Crystal Properties Matthews coefficient Solvent content 1.95 36.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.39 α = 90 b = 42.39 β = 90 c = 216.404 γ = 90
Symmetry Space Group P 43 2 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 PIXEL DECTRIS PILATUS3 6M 2019-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 1.61 42.39 99.3 0.035 1 34.32 12.7 26714 27.19
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 1.61 1.71 0.499 0.992 5.07
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 5GPI 1.61 42.39 1.38 26639 1332 98.98 0.1869 0.1858 0.1855 0.2096 0.2092 35.17
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 11.2116 f_angle_d 0.7709 f_chiral_restr 0.055 f_plane_restr 0.0055 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1415 Nucleic Acid Atoms Solvent Atoms 134 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement XDS data scaling XDS data reduction PHASER phasing Coot model building