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Structure of the midlink and cap-binding domains of influenza B polymerase PB2 subunit with a bound azaindazole cap-binding inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WSA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Crystals were obtained by mixing FluB double domain at 15 mg/ml in 50 mM Tris pH 7.5 and 10% glycerol and 5 mM of VX-787 with 0.1 M PTCP and 25% PEG1500.
Crystal Properties Matthews coefficient Solvent content 2.43 49.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.2 α = 90 b = 73.2 β = 90 c = 103.74 γ = 120
Symmetry Space Group P 31 2 1
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 2017-03-02 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 Merge 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 2.05 50 99.7 0.119 0.997 10.46 5.7 20671
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.15 99.7 1.1 0.644 1.75 5.78
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 4WSA 2.05 40.14 19649 1022 99.71 0.23065 0.22945 0.2311 0.25404 0.2577 RANDOM 50.898
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] 11.63 11.63 -23.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.88 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_4_deg 10.984 r_dihedral_angle_1_deg 5.398 r_long_range_B_refined 4.835 r_long_range_B_other 4.715 r_mcangle_it 2.517 r_mcangle_other 2.516 r_scangle_other 2.379 r_mcbond_it 1.433
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.88 r_dihedral_angle_3_deg 12.172 r_dihedral_angle_4_deg 10.984 r_dihedral_angle_1_deg 5.398 r_long_range_B_refined 4.835 r_long_range_B_other 4.715 r_mcangle_it 2.517 r_mcangle_other 2.516 r_scangle_other 2.379 r_mcbond_it 1.433 r_mcbond_other 1.433 r_scbond_it 1.351 r_scbond_other 1.351 r_angle_refined_deg 1.07 r_angle_other_deg 0.835 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 1792 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing