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PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with NegAcid3-Am03
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 4.8 298 30% w/v PEG 2000, 0.2M Ammonium sulfate, 0.1M acetate (pH 4.8)
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.581 α = 90 b = 42.581 β = 90 c = 216.368 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 EIGER2 XE 9M 2023-10-10 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 1.83 54.11 100 0.171 0.175 0.035 0.998 6.8 25.4 18759
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 1.83 1.87 99.9 5.454 5.557 1.061 0.207 27
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 1.83 54.09 16249 838 91.51 0.2427 0.23944 0.2487 0.30459 0.306 RANDOM 54.396
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] 1.7 1.7 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.989 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 15.667 r_long_range_B_refined 15.135 r_long_range_B_other 15.117 r_dihedral_angle_1_deg 7.524 r_scangle_other 6.731 r_mcangle_other 6.275 r_mcangle_it 6.27 r_scbond_other 4.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.989 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 15.667 r_long_range_B_refined 15.135 r_long_range_B_other 15.117 r_dihedral_angle_1_deg 7.524 r_scangle_other 6.731 r_mcangle_other 6.275 r_mcangle_it 6.27 r_scbond_other 4.296 r_scbond_it 4.287 r_mcbond_other 4.061 r_mcbond_it 3.97 r_angle_refined_deg 1.526 r_angle_other_deg 1.18 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 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 1476 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction