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Crystal structure of the Ilheus virus helicase: implications for enzyme function and drug design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289.15 0.1 M tris hydrochloride, pH 8.5, 0.2 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.45 49.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.213 α = 90 b = 112.213 β = 90 c = 76.459 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 289.15 PIXEL DECTRIS PILATUS3 6M 2020-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 1.75 50 99.9 0.071 43.3 11.3 49792
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 1.75 1.81 0.293
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2WV9 1.75 35.51 47267 2464 99.86 0.1587 0.1567 0.1981 0.2059 RANDOM 20.093
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] 0.28 0.28 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.371 r_dihedral_angle_4_deg 16.291 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.366 r_angle_refined_deg 1.729 r_angle_other_deg 1.47 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.371 r_dihedral_angle_4_deg 16.291 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.366 r_angle_refined_deg 1.729 r_angle_other_deg 1.47 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3456 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHENIX phasing