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Structure of the midlink and cap-binding domains of influenza A polymerase PB2 subunit with a bound azaindole cap-binding inhibitor (VX-787)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6EUX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 Crystals were obtained by mixing protein at 16 mg per mL mixed with 2 mM VX-787 in 0.1 M MES pH6, 0.7 M sodium formate pH 6.
Crystal Properties Matthews coefficient Solvent content 3.05 59.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.49 α = 89.54 b = 80.32 β = 107.12 c = 92.32 γ = 99.11
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-F 2017-10-03 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 2.7 50 94.8 0.091 0.991 5.99 1.69 38468
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 2.7 2.77 94.2 0.698 0.508 1.02 1.55
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 6EUX 2.7 43.35 36631 1837 94.83 0.24469 0.2428 0.2461 0.28168 0.2889 RANDOM 49.627
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] -0.24 0.95 -1.09 3.2 0.72 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_4_deg 15.992 r_long_range_B_refined 7.623 r_long_range_B_other 7.622 r_dihedral_angle_1_deg 6.377 r_scangle_other 5.062 r_mcangle_it 4.93 r_mcangle_other 4.93 r_scbond_it 3.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.89 r_dihedral_angle_3_deg 16.121 r_dihedral_angle_4_deg 15.992 r_long_range_B_refined 7.623 r_long_range_B_other 7.622 r_dihedral_angle_1_deg 6.377 r_scangle_other 5.062 r_mcangle_it 4.93 r_mcangle_other 4.93 r_scbond_it 3.105 r_scbond_other 3.105 r_mcbond_it 3.062 r_mcbond_other 3.053 r_angle_refined_deg 1.491 r_angle_other_deg 0.953 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 8713 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing