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Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP
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, 0.2 M sodium acetate truhydrate, 20% w/v PEG 3350, 10% v/v ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.45 49.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.12 α = 90 b = 73.12 β = 90 c = 196.124 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 2.099 50 99.9 0.067 0.999 24.38 14.3 32056
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.099 2.23 99.7 0.99 0.839 2.53
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 2.099 45.778 32056 1565 99.888 0.234 0.2329 0.2329 0.259 0.2583 57.908
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] 1.42 1.42 -2.839
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.025 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 14.533 r_lrange_it 9.815 r_scangle_it 7.951 r_dihedral_angle_1_deg 7.27 r_mcangle_it 6.769 r_scbond_it 5.637 r_mcbond_it 5.049 r_angle_refined_deg 1.619
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.025 r_dihedral_angle_4_deg 18.024 r_dihedral_angle_3_deg 14.533 r_lrange_it 9.815 r_scangle_it 7.951 r_dihedral_angle_1_deg 7.27 r_mcangle_it 6.769 r_scbond_it 5.637 r_mcbond_it 5.049 r_angle_refined_deg 1.619 r_nbtor_refined 0.305 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.213 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.111 r_symmetry_xyhbond_nbd_refined 0.105 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3414 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing