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Crystal Structure of Dengue Virus 1 NS2B/NS3 protease
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 7.5 293 0.1M HEPES pH 7.5, 12% PEG 3350 and 0.005M each of NiCl2, CdCl2, MgCl2 and CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.721 α = 90 b = 60.848 β = 90 c = 161.644 γ = 90
Symmetry Space Group I 2 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 CCD MARMOSAIC 325 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.9497 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 40 14424
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 2FOM 2.2 28.95 13704 720 99.1 0.242 0.239 0.2468 0.284 0.2718 RANDOM 45.84
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] 0.02 -0.04 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.654 r_dihedral_angle_3_deg 16.333 r_dihedral_angle_4_deg 15.587 r_dihedral_angle_1_deg 7.865 r_scangle_it 5.374 r_scbond_it 3.425 r_mcangle_it 2.475 r_angle_refined_deg 1.88 r_mcbond_it 1.375 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.654 r_dihedral_angle_3_deg 16.333 r_dihedral_angle_4_deg 15.587 r_dihedral_angle_1_deg 7.865 r_scangle_it 5.374 r_scbond_it 3.425 r_mcangle_it 2.475 r_angle_refined_deg 1.88 r_mcbond_it 1.375 r_chiral_restr 0.129 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1471 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 9
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling