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Crystal structure of Zika virus NS2B-NS3 protease in apo-form.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LC0 PDB-5LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 12.8mg/ml, 1M Sodium chloride, 0.05M Tris-HCl pH=8.5;
Scrren: Classics II (H3), 0.24M Sodium malonate pH=7.0, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.63 24.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.086 α = 90 b = 55.086 β = 90 c = 249.2 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 CCD MARMOSAIC 300 mm CCD C(111) 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97856 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 3.1 30 100 0.115 0.115 17.8 6.8 7675 -3 79.3
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 3.1 3.15 100 0.732 0.925 2.74 6.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB-5LC0 3.1 29.9 6875 739 99.79 0.22862 0.22263 0.28755 0.2708 RANDOM 93.348
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] 3.67 3.67 -7.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.108 r_dihedral_angle_3_deg 8.947 r_dihedral_angle_4_deg 6.305 r_long_range_B_other 4.84 r_long_range_B_refined 4.839 r_mcangle_it 2.817 r_mcangle_other 2.816 r_scangle_other 2.134 r_mcbond_it 1.583 r_mcbond_other 1.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 16.108 r_dihedral_angle_3_deg 8.947 r_dihedral_angle_4_deg 6.305 r_long_range_B_other 4.84 r_long_range_B_refined 4.839 r_mcangle_it 2.817 r_mcangle_other 2.816 r_scangle_other 2.134 r_mcbond_it 1.583 r_mcbond_other 1.583 r_dihedral_angle_1_deg 1.58 r_angle_refined_deg 1.247 r_scbond_it 1.212 r_scbond_other 1.212 r_angle_other_deg 0.824 r_chiral_restr 0.069 r_gen_planes_refined 0.021 r_gen_planes_other 0.018 r_bond_refined_d 0.006 r_bond_other_d 0.001 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 2442 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing