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DengueV-2 Capsid ST148 inhibitor Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SFK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 291 3.0 M NaNO3, 100 mM HEPES pH 6.8, 5% glycerol
Crystal Properties Matthews coefficient Solvent content 1.87 34.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.4 α = 90 b = 25.5 β = 92.55 c = 68.5 γ = 90
Symmetry Space Group P 1 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 EIGER X 9M 2018-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.07812 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.5 50 93.4 0.094 0.103 0.042 8.7 6.1 21285
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 1.5 1.53 75.9 0.829 0.91 0.369 0.695 5.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1sfk 1.5 40.39 19240 973 88.57 0.1478 0.1454 0.1455 0.1937 0.1936 RANDOM 17.535
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] 0.16 -0.07 -0.05 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_3_deg 12.335 r_dihedral_angle_4_deg 12.07 r_dihedral_angle_1_deg 4.847 r_mcangle_it 2.124 r_angle_refined_deg 1.629 r_mcbond_it 1.585 r_mcbond_other 1.582 r_angle_other_deg 1.323 r_rigid_bond_restr 1.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.452 r_dihedral_angle_3_deg 12.335 r_dihedral_angle_4_deg 12.07 r_dihedral_angle_1_deg 4.847 r_mcangle_it 2.124 r_angle_refined_deg 1.629 r_mcbond_it 1.585 r_mcbond_other 1.582 r_angle_other_deg 1.323 r_rigid_bond_restr 1.102 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1309 Nucleic Acid Atoms Solvent Atoms 54 Heterogen Atoms 126
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction