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Crystal structure of the tick-borne encephalitis virus NS3 helicase in complex with ADP-Pi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BM0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Bis Tris Propane, 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 2.4 49.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.98 α = 90 b = 72.98 β = 90 c = 196.586 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 2021-03-10 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 2.097 48.81 99.5 0.99 23.02 13.67 31603
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 2.1 2.22 99.5 0.904 3.21
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 7BM0 2.1 48.806 31594 1547 98.396 0.216 0.2138 0.2211 0.2507 0.2571 39.018
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] 1.072 1.072 -2.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.914 r_dihedral_angle_4_deg 16.913 r_dihedral_angle_3_deg 14.714 r_lrange_other 7.95 r_lrange_it 7.873 r_dihedral_angle_1_deg 7.53 r_scangle_it 6.762 r_scangle_other 6.761 r_mcangle_it 5.111 r_mcangle_other 5.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.914 r_dihedral_angle_4_deg 16.913 r_dihedral_angle_3_deg 14.714 r_lrange_other 7.95 r_lrange_it 7.873 r_dihedral_angle_1_deg 7.53 r_scangle_it 6.762 r_scangle_other 6.761 r_mcangle_it 5.111 r_mcangle_other 5.11 r_scbond_it 4.36 r_scbond_other 4.356 r_mcbond_it 3.565 r_mcbond_other 3.56 r_angle_other_deg 2.363 r_angle_refined_deg 1.54 r_nbd_other 0.323 r_symmetry_nbd_other 0.219 r_nbd_refined 0.204 r_nbtor_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.146 r_symmetry_nbd_refined 0.1 r_chiral_restr 0.076 r_symmetry_nbtor_other 0.071 r_bond_other_d 0.035 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_symmetry_xyhbond_nbd_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3390 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing