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PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with NegAcid3-Am02
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 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.62 α = 90 b = 42.62 β = 90 c = 216.85 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 1.92 216.85 99.9 0.174 0.179 0.038 0.999 9 21.5 16393
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 1.92 1.97 100 8.043 8.266 1.888 0.363 18.9
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.92 42.66 15371 782 98.96 0.23138 0.22858 0.28398 0.2792 RANDOM 61.834
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] 3.12 3.12 -6.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.772 r_dihedral_angle_4_deg 16.181 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 11.794 r_long_range_B_other 11.702 r_dihedral_angle_1_deg 7.367 r_scangle_other 7.115 r_mcangle_it 6.18 r_mcangle_other 6.178 r_scbond_other 4.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.772 r_dihedral_angle_4_deg 16.181 r_dihedral_angle_3_deg 14.91 r_long_range_B_refined 11.794 r_long_range_B_other 11.702 r_dihedral_angle_1_deg 7.367 r_scangle_other 7.115 r_mcangle_it 6.18 r_mcangle_other 6.178 r_scbond_other 4.505 r_scbond_it 4.498 r_mcbond_other 4.254 r_mcbond_it 4.128 r_angle_refined_deg 1.409 r_angle_other_deg 1.169 r_chiral_restr 0.051 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 1476 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction