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Structure of dengue virus protease with an allosteric Inhibitor that blocks replication
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FOM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 35% PEG 200, 100 mM MES, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.155 α = 90 b = 109.155 β = 90 c = 76.003 γ = 120
Symmetry Space Group P 3 2 1
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 PILATUS3 X 6M 2018-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.6 50 100 0.211 19.93 9.8 16509
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.69 100 1.943 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2FOM 2.8 47.31 12544 670 99.95 0.24558 0.24228 0.30997 0.2765 RANDOM 66.263
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] -3.41 -1.7 -3.41 11.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.996 r_dihedral_angle_3_deg 29.265 r_dihedral_angle_4_deg 20.725 r_long_range_B_refined 11.938 r_long_range_B_other 11.937 r_mcangle_other 11.7 r_mcangle_it 11.698 r_scangle_other 11.499 r_scbond_it 9.093 r_scbond_other 9.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.996 r_dihedral_angle_3_deg 29.265 r_dihedral_angle_4_deg 20.725 r_long_range_B_refined 11.938 r_long_range_B_other 11.937 r_mcangle_other 11.7 r_mcangle_it 11.698 r_scangle_other 11.499 r_scbond_it 9.093 r_scbond_other 9.09 r_mcbond_it 9.071 r_mcbond_other 9.063 r_rigid_bond_restr 6.123 r_dihedral_angle_1_deg 4.575 r_angle_other_deg 1.737 r_angle_refined_deg 1.503 r_chiral_restr 0.072 r_bond_other_d 0.018 r_bond_refined_d 0.014 r_gen_planes_refined 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2512 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing