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Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to a 22-mer modified Pol II CTD peptide with serine 5 thiophosphorylated.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M3H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Bat FluA polymerase bound to the ends of the RNA promotor (5 prime end nts 1-16, 3 prime end nts 1-18) was co-crystallized in a 1:8 ratio with the thiophospho-serine-5 22-mer Pol II CTD peptide mimic in 0.8 M sodium-potassium phosphate at pH 5.0. Crystals were set at 4 C using seeding.
Crystal Properties Matthews coefficient Solvent content 3.09 60.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 267.77 α = 90 b = 147.81 β = 97.08 c = 88.41 γ = 90
Symmetry Space Group C 1 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 PILATUS 6M-F 2017-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.97242 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 2.7 50 98.6 0.049 0.996 14.34 2.92 92066
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 2.7 2.77 96.7 0.5 0.761 1.87 2.69
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 5m3h 2.7 50 87532 4534 98.6 0.21514 0.2129 0.2177 0.25763 0.2552 RANDOM 90.198
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] 3.28 3.39 -3.86 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_4_deg 12.669 r_long_range_B_refined 7.864 r_long_range_B_other 7.861 r_dihedral_angle_1_deg 5.741 r_mcangle_it 4.887 r_mcangle_other 4.887 r_scangle_other 4.758 r_mcbond_it 2.923
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_3_deg 14.455 r_dihedral_angle_4_deg 12.669 r_long_range_B_refined 7.864 r_long_range_B_other 7.861 r_dihedral_angle_1_deg 5.741 r_mcangle_it 4.887 r_mcangle_other 4.887 r_scangle_other 4.758 r_mcbond_it 2.923 r_mcbond_other 2.923 r_scbond_it 2.778 r_scbond_other 2.751 r_angle_refined_deg 1.085 r_angle_other_deg 0.874 r_chiral_restr 0.062 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 17644 Nucleic Acid Atoms 600 Solvent Atoms 137 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing