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Crystal structure of apo NS3 helicase from tick-borne encephalitis virus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6ADW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Bis Tris Propane pH 6.5, 0.2 M Sodium acetate trihydrate, 20% w/v PEG 3350, 10% v/v Ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.47 50.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.298 α = 90 b = 73.298 β = 90 c = 196.048 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2020-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918400 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.828 49.06 99.9 1 2.22 20 48205
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.94 99.3 0.865
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6ADW 1.828 49.06 48205 2366 99.83 0.183 0.1808 0.1853 0.2291 0.2354 43.364
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] -0.029 -0.029 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.291 r_dihedral_angle_4_deg 20.65 r_dihedral_angle_3_deg 14.902 r_scangle_it 10.912 r_scangle_other 10.91 r_lrange_other 10.058 r_lrange_it 10.045 r_scbond_it 9.855 r_scbond_other 9.853 r_rigid_bond_restr 9.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.291 r_dihedral_angle_4_deg 20.65 r_dihedral_angle_3_deg 14.902 r_scangle_it 10.912 r_scangle_other 10.91 r_lrange_other 10.058 r_lrange_it 10.045 r_scbond_it 9.855 r_scbond_other 9.853 r_rigid_bond_restr 9.358 r_mcangle_it 8.663 r_mcangle_other 8.662 r_mcbond_it 8.003 r_mcbond_other 7.997 r_dihedral_angle_1_deg 7.678 r_angle_refined_deg 1.934 r_angle_other_deg 1.802 r_nbd_refined 0.22 r_symmetry_nbd_other 0.22 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.137 r_symmetry_xyhbond_nbd_refined 0.129 r_nbd_other 0.128 r_chiral_restr 0.108 r_symmetry_nbtor_other 0.086 r_symmetry_nbd_refined 0.065 r_bond_other_d 0.018 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3366 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing