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Crystal structure of Zika NS2B-NS3 protease in complex with follow-up compound EOS41783 from ECBL
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZUM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 24 % (w/v) PEG 2000
Crystal Properties Matthews coefficient Solvent content 1.99 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.55 α = 90 b = 60.55 β = 90 c = 214.88 γ = 90
Symmetry Space Group P 43 21 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 2024-10-22 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 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 46.24 100 0.102 0.107 0.999 14.7 11.27 53981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 100 1.156 1.207 0.721 1.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.6 40.18 1.37 53977 2099 99.98 0.1822 0.1809 0.1816 0.2164 0.2166
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 13.573 f_angle_d 0.959 f_chiral_restr 0.069 f_bond_d 0.008 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2911 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing