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NS2B-NS3 protease from dengue virus in the presence of DTNB, a covalent allosteric inhibitor
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 8.5 298 40% PEG200, 0.1 M Acetic acid, pH 5.5. Crystals were soaked in 40% PEG200, 0.1 M Tris pH 8.5, 5 mM 5,5'-dithiobis-(2-nitrobenzoic acid) (DTNB), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.07 40.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.394 α = 90 b = 62.09 β = 90 c = 114.347 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.979 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.74 43.7 85.3 0.114 0.114 30.1 6.3 19456 19455 2 3 32.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 85.3 0.114 0.114 1.85 4.6 19456
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 2FOM 1.74 43.66 10000 10000 19455 18265 996 85 0.217 0.215 0.2062 0.241 0.2277 random 28.8415
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] -0.141 0.337 -0.196
RMS Deviations Key Refinement Restraint Deviation o_scangle_it 13.44 o_scbond_it 11.98 o_mcangle_it 7.88 o_mcbond_it 7.02 o_angle_deg 1.915 o_improper_angle_d 0.423 o_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1535 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 1
Software Software Software Name Purpose PHASER phasing PRIME-X refinement HKL-2000 data reduction HKL-2000 data scaling