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Dengue virus 4 NS3 helicase in complex with ssRNA and AMPPNP
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 1.98 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.66 α = 90 b = 105.192 β = 117.66 c = 72.435 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 2.3 2.4 99.3 0.13 11.6 4.9 44454 2
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 2.3 2.4 98.6 0.5 2.7 4.8
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 PDB ENTRY 2JLU 1.9 20 57632 3105 87.61 0.19349 0.19049 0.2021 0.24801 0.2571 RANDOM 25.077
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] 1.43 0.6 -1.11 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 16.588 r_dihedral_angle_3_deg 16.108 r_dihedral_angle_1_deg 5.813 r_scangle_it 2.153 r_scbond_it 1.354 r_angle_refined_deg 1.338 r_mcangle_it 0.941 r_mcbond_it 0.565 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.696 r_dihedral_angle_4_deg 16.588 r_dihedral_angle_3_deg 16.108 r_dihedral_angle_1_deg 5.813 r_scangle_it 2.153 r_scbond_it 1.354 r_angle_refined_deg 1.338 r_mcangle_it 0.941 r_mcbond_it 0.565 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.196 r_symmetry_hbond_refined 0.148 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 7218 Nucleic Acid Atoms 256 Solvent Atoms 716 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling