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Crystal structure of Zika Virus NS2B-NS3 protease in complex with an allosteric inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LC0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 0.10 M Tris pH=7.00
30.00 %w/v PEG 3K
0.20 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.688 α = 90 b = 90.351 β = 90 c = 96.189 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 PILATUS 6M-F 2020-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999926421265 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.17 65.86 59.56 0.994 5.6 8.2 5331
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.17 3.54 0.737
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.18 65.86 5101 230 59.56 0.28334 0.28124 0.2805 0.33009 0.3309 RANDOM 73.9
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] -0.66 -0.86 1.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.273 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_4_deg 12.067 r_dihedral_angle_1_deg 4.395 r_long_range_B_refined 2.471 r_long_range_B_other 2.471 r_mcangle_it 1.046 r_mcangle_other 1.046 r_angle_refined_deg 1.042 r_angle_other_deg 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.273 r_dihedral_angle_3_deg 13.811 r_dihedral_angle_4_deg 12.067 r_dihedral_angle_1_deg 4.395 r_long_range_B_refined 2.471 r_long_range_B_other 2.471 r_mcangle_it 1.046 r_mcangle_other 1.046 r_angle_refined_deg 1.042 r_angle_other_deg 0.891 r_scangle_other 0.571 r_mcbond_it 0.551 r_mcbond_other 0.551 r_scbond_it 0.272 r_scbond_other 0.272 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 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 2427 Nucleic Acid Atoms Solvent Atoms 15 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement XDS data reduction pointless data scaling PHASER phasing