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CRYSTAL STRUCTURE OF THE ZIKA VIRUS NS2B-NS3 PROTEASE in super-open conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IJO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.6 mM protein, in 100 mM NaCl, 1.0 mM TCEP, 20 mM Tris-Cl buffer (pH 8.0) was mixed with the well solution (25% PEG3330, 200 mM NaCl and 100 mM BisTris pH 6.5)
Crystal Properties Matthews coefficient Solvent content 1.85 33.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.956 α = 90 b = 54.956 β = 90 c = 250.108 γ = 90
Symmetry Space Group P 41 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 2016-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97946 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 38.4 99.8 0.137 0.998 11.6 8.1 8410
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 3 3.18 100 1.68 0.71 1.1 8.6
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-Factor (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 THROUGHOUT 2IJO 3 38.4 7918 436 99.69 0.21293 0.2103 0.2153 0.25931 0.256 RANDOM 111.109
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] 2.85 2.85 -5.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_3_deg 20.08 r_dihedral_angle_4_deg 16.37 r_long_range_B_refined 14.424 r_long_range_B_other 14.423 r_mcangle_it 8.464 r_mcangle_other 8.463 r_scangle_other 8.182 r_dihedral_angle_1_deg 6.745 r_mcbond_it 5.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_3_deg 20.08 r_dihedral_angle_4_deg 16.37 r_long_range_B_refined 14.424 r_long_range_B_other 14.423 r_mcangle_it 8.464 r_mcangle_other 8.463 r_scangle_other 8.182 r_dihedral_angle_1_deg 6.745 r_mcbond_it 5.207 r_mcbond_other 5.206 r_scbond_it 4.957 r_scbond_other 4.955 r_angle_refined_deg 1.884 r_angle_other_deg 1.373 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2469 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing