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Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0015373
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 298 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.42 α = 90 b = 42.42 β = 90 c = 215.96 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 2023-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92124 Diamond I04-1
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 1.95 42.456 100 0.118 0.124 0.04 0.999 13.9 17 15473
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) 1 1.95 2 2.994 3.158 1 0.654 18.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.95 42.456 15393 786 99.968 0.218 0.2152 0.2782 0.2705 48.782
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] 1.264 1.264 -2.529
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 23.082 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_1_deg 7.956 r_lrange_it 5.273 r_lrange_other 5.272 r_scangle_it 2.756 r_scangle_other 2.754 r_mcangle_it 2.294 r_mcangle_other 2.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_4_deg 23.082 r_dihedral_angle_3_deg 15.83 r_dihedral_angle_1_deg 7.956 r_lrange_it 5.273 r_lrange_other 5.272 r_scangle_it 2.756 r_scangle_other 2.754 r_mcangle_it 2.294 r_mcangle_other 2.293 r_scbond_it 1.741 r_scbond_other 1.74 r_angle_refined_deg 1.586 r_mcbond_it 1.443 r_mcbond_other 1.436 r_angle_other_deg 1.267 r_nbd_other 0.203 r_nbd_refined 0.186 r_symmetry_nbd_other 0.185 r_xyhbond_nbd_refined 0.167 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbd_refined 0.117 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1438 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing