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Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0036543
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PN6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.484 α = 90 b = 42.484 β = 90 c = 218.029 γ = 90
Symmetry Space Group P 43 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 EIGER X 9M 2025-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9212 Diamond I04-1
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 1.45 54.567 100 1 24.9 1.8 36991
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 1.45 1.47 0.714 1.9
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 1.45 54.567 36879 1863 99.957 0.196 0.1945 0.1911 0.2222 0.2176 30.58
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] 0.914 0.914 -1.829
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_4_deg 15.021 r_dihedral_angle_3_deg 11.412 r_dihedral_angle_1_deg 7.867 r_lrange_it 4.958 r_lrange_other 4.842 r_scangle_it 2.941 r_scangle_other 2.94 r_scbond_it 1.954 r_scbond_other 1.953
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.698 r_dihedral_angle_4_deg 15.021 r_dihedral_angle_3_deg 11.412 r_dihedral_angle_1_deg 7.867 r_lrange_it 4.958 r_lrange_other 4.842 r_scangle_it 2.941 r_scangle_other 2.94 r_scbond_it 1.954 r_scbond_other 1.953 r_mcangle_other 1.759 r_mcangle_it 1.758 r_angle_refined_deg 1.741 r_angle_other_deg 1.469 r_mcbond_it 1.189 r_mcbond_other 1.176 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_other 0.212 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.187 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.161 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_chiral_restr_other 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1444 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling PHASER phasing