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Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AY4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Bis Tris Propane pH 6.5, 0.02 M sodium potassium phosphate pH. 7.5, 20% w/v PEG 3350, 10% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.952 α = 90 b = 72.952 β = 90 c = 196.45 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 PILATUS3 S 6M 2020-12-10 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) Rrim I (All) 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 1.9 45.71 99.9 0.083 0.999 19.1 14.25 43006
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 1.9 2 99.7 0.795 2.03 14.64
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 7AY4 1.9 45.71 43006 959 99.916 0.217 0.2162 0.2148 0.2294 0.2431 42.597
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] 0.679 0.679 -1.357
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.289 r_dihedral_angle_4_deg 20.263 r_dihedral_angle_3_deg 15.435 r_rigid_bond_restr 7.214 r_dihedral_angle_1_deg 7.162 r_angle_refined_deg 1.765 r_nbtor_refined 0.299 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.289 r_dihedral_angle_4_deg 20.263 r_dihedral_angle_3_deg 15.435 r_rigid_bond_restr 7.214 r_dihedral_angle_1_deg 7.162 r_angle_refined_deg 1.765 r_nbtor_refined 0.299 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.183 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.111 r_chiral_restr 0.079 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_mcbond_it r_mcangle_it r_scbond_it r_scangle_it r_lrange_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3369 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing