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Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor, baloxavir acid (BXA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FML PDB:5FML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein, at 15-17 mg/ml, was incubated with 10-fold molar excess of BXA for 30 min at RT, mixtures were centrifuged at RT for 5 minutes at 12000 g, and soluble fraction was used for crystallization trials (final protein concentration 8-10 mg/ml).
Mother liquor was 0.2 M CaCl2, 0.1 M MES pH 6.0, 20% (w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.71 54.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.71 α = 90 b = 63.71 β = 90 c = 125.41 γ = 90
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 2M 2017-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 2.28 56.8 93.5 0.044 0.999 16.1 4.4 10663
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.28 2.34 0.561 0.899 2.37
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB:5FML 2.28 56.8 10147 516 93.44 0.18177 0.17911 0.1923 0.23541 0.2421 RANDOM 62.623
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] 2.55 2.55 -5.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.617 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.695 r_long_range_B_refined 11.299 r_long_range_B_other 11.297 r_scangle_other 9.53 r_mcangle_other 7.343 r_mcangle_it 7.342 r_scbond_it 6.599 r_scbond_other 6.595
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.617 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.695 r_long_range_B_refined 11.299 r_long_range_B_other 11.297 r_scangle_other 9.53 r_mcangle_other 7.343 r_mcangle_it 7.342 r_scbond_it 6.599 r_scbond_other 6.595 r_dihedral_angle_1_deg 6.181 r_mcbond_it 5.464 r_mcbond_other 5.449 r_angle_refined_deg 1.824 r_angle_other_deg 1.064 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1494 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing