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Dengue virus 4 NS3 helicase structure, apo enzyme.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMF PDB ENTRY 2BMF
Crystallization Crystal Properties Matthews coefficient Solvent content 2.23 44.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.821 α = 90 b = 92.614 β = 90 c = 102.962 γ = 90
Symmetry Space Group P 21 21 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 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 1.7 21.1 99.5 0.04 22.4 7.5 59272 2.7
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 1.7 1.8 95.8 0.76 2.7 7.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2BMF 1.67 20.96 56198 2989 99.63 0.21212 0.21095 0.2074 0.23384 0.2316 RANDOM 28.553
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] 0.08 0.21 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_3_deg 13.653 r_dihedral_angle_4_deg 11.608 r_dihedral_angle_1_deg 6.387 r_scangle_it 1.962 r_scbond_it 1.193 r_mcangle_it 0.823 r_mcbond_it 0.485 r_angle_refined_deg 0.41 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.06 r_dihedral_angle_3_deg 13.653 r_dihedral_angle_4_deg 11.608 r_dihedral_angle_1_deg 6.387 r_scangle_it 1.962 r_scbond_it 1.193 r_mcangle_it 0.823 r_mcbond_it 0.485 r_angle_refined_deg 0.41 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.119 r_symmetry_hbond_refined 0.097 r_chiral_restr 0.036 r_gen_planes_refined 0.005 r_bond_refined_d 0.002 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 3591 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling