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PanDDA analysis group deposition -- Crystal Structure of ZIKV NS2B-NS3 protease in complex with ASAP-0014704-001
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 2.11 41.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.503 α = 90 b = 42.503 β = 90 c = 216.415 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 2023-09-19 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 1.48 216.48 100 0.103 0.105 0.021 0.999 10.9 24.6 34587
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.51 99.7 11.905 2.658 0.182 19.3
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 1.48 54.1 29154 1550 89.12 0.24049 0.23826 0.2454 0.28299 0.282 RANDOM 47.451
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] -0.2 -0.2 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_long_range_B_other 22.97 r_long_range_B_refined 22.932 r_dihedral_angle_4_deg 20.757 r_dihedral_angle_3_deg 14.826 r_dihedral_angle_1_deg 7.695 r_scangle_other 2.743 r_mcangle_it 2.533 r_mcangle_other 2.532 r_angle_refined_deg 1.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.041 r_long_range_B_other 22.97 r_long_range_B_refined 22.932 r_dihedral_angle_4_deg 20.757 r_dihedral_angle_3_deg 14.826 r_dihedral_angle_1_deg 7.695 r_scangle_other 2.743 r_mcangle_it 2.533 r_mcangle_other 2.532 r_angle_refined_deg 1.921 r_scbond_other 1.67 r_scbond_it 1.662 r_angle_other_deg 1.43 r_mcbond_other 1.416 r_mcbond_it 1.395 r_chiral_restr 0.088 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.008 r_gen_planes_other 0.005 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 101 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement BUSTER refinement Aimless data scaling PHASER phasing XDS data reduction XDS data reduction XDS data reduction XDS data reduction XDS data reduction