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Crystal Structure of Unlinked NS2B-NS3 Protease from Zika Virus in Complex with Inhibitor MI-2128
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
18 % PEG2000
Crystal Properties Matthews coefficient Solvent content 2.44 49.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.622 α = 90 b = 60.563 β = 90 c = 80.883 γ = 90
Symmetry Space Group P 21 21 21
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 S 6M 2020-06-27 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 1.45 48.48 99.9 0.046 0.999 21.59 7.25 43944 24.58
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 1.45 1.54 99.7 0.505 0.929 3.4 7.12
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 1.45 42.31 1.36 43935 2196 99.87 0.1491 0.1479 0.1561 0.1748 0.1839 34.03
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 15.3797 f_angle_d 0.9609 f_chiral_restr 0.09 f_bond_d 0.0068 f_plane_restr 0.0053
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1394 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 58
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building