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Dengue virus 4 NS3 helicase in complex with ssRNA and ADP-Phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLU PDB ENTRY 2JLU
Crystallization Crystal Properties Matthews coefficient Solvent content 2.01 38.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.748 α = 90 b = 105.591 β = 117.68 c = 72.671 γ = 90
Symmetry Space Group C 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 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE
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 2.4 40.8 99.6 0.14 13.8 5.5 188211 1
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 2.4 2.5 97.5 0.72 1.7 5.1
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 PDB ENTRY 2JLU 2.4 19.99 32553 1726 99.63 0.20194 0.19911 0.25494 0.2366 RANDOM 35.621
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] 0.13 0.04 -0.12 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.981 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_4_deg 14.062 r_dihedral_angle_1_deg 6.313 r_scangle_it 1.391 r_angle_refined_deg 1.134 r_scbond_it 0.799 r_mcangle_it 0.622 r_mcbond_it 0.352 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.981 r_dihedral_angle_3_deg 15.424 r_dihedral_angle_4_deg 14.062 r_dihedral_angle_1_deg 6.313 r_scangle_it 1.391 r_angle_refined_deg 1.134 r_scbond_it 0.799 r_mcangle_it 0.622 r_mcbond_it 0.352 r_nbtor_refined 0.296 r_xyhbond_nbd_refined 0.268 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.163 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7185 Nucleic Acid Atoms 296 Solvent Atoms 380 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling