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Crystal structure of Zika Virus NS2B-NS3 protease in complex with compound 1
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 277.15 10% Isopropanol
0.14 M LiSO4
0.10 M Sodium phosphate citrate
Crystal Properties Matthews coefficient Solvent content 2.96 58.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.575 α = 90 b = 91.546 β = 90 c = 103.844 γ = 90
Symmetry Space Group I 2 2 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 PILATUS 6M-F 2020-09-17 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) R Merge I (Observed) Rrim I (All) Rpim 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 2.48 68.671 90.9 0.1302 0.1399 0.0502 0.988 9.13 7.72 5729
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.48 2.692 58.7 1.4321 1.5321 0.5391 0.644 1.26 7.77 286
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.48 68.671 5729 269 55.012 0.249 0.247 0.2524 0.2959 0.3013 54.642
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] -0.641 -1.464 2.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.834 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_6_deg 9.939 r_dihedral_angle_other_3_deg 9.132 r_lrange_it 6.809 r_lrange_other 6.807 r_dihedral_angle_1_deg 5.795 r_mcangle_it 3.552 r_mcangle_other 3.551 r_scangle_it 2.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.834 r_dihedral_angle_3_deg 12.295 r_dihedral_angle_6_deg 9.939 r_dihedral_angle_other_3_deg 9.132 r_lrange_it 6.809 r_lrange_other 6.807 r_dihedral_angle_1_deg 5.795 r_mcangle_it 3.552 r_mcangle_other 3.551 r_scangle_it 2.389 r_scangle_other 2.388 r_mcbond_it 1.938 r_mcbond_other 1.932 r_scbond_it 1.265 r_scbond_other 1.264 r_angle_refined_deg 1.075 r_angle_other_deg 0.484 r_nbtor_refined 0.16 r_symmetry_nbd_other 0.155 r_nbd_refined 0.133 r_symmetry_nbd_refined 0.122 r_xyhbond_nbd_refined 0.12 r_nbd_other 0.089 r_symmetry_nbtor_other 0.072 r_chiral_restr 0.047 r_symmetry_xyhbond_nbd_refined 0.025 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1369 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 70
Software Software Software Name Purpose autoPROC data processing autoPROC data processing Aimless data scaling autoPROC data processing REFMAC refinement XDS data reduction PHASER phasing