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Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer and CTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MSG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.4 277 Influenza B polymerase at 9 mg per ml in was mixed with 40 microM vRNA 5 prime end 14-mer, 40 microM vRNA 3 prime end 21-mer and 80 microM 14-mer capped RNA. The mother liquor contained 200 mM di-ammonium phosphate and 100 mM sodium acetate between pH 4.0 and 4.4. CTP was soaked for 18 hours into grown crystals at a final concentration of 5 mM in the drop.
Crystal Properties Matthews coefficient Solvent content 5.31 76.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.191 α = 90 b = 200.191 β = 90 c = 256.208 γ = 120
Symmetry Space Group P 32 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 2018-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.977 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.24 50 67.9 0.175 0.189 0.996 7.6 6.9 64019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.24 3.48 60.8 1.19 1.28 0.65 1.5 7.3
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 5MSG 3.24 50 60950 3069 67.65 0.20995 0.20868 0.2074 0.23448 0.2298 RANDOM 116.801
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] -2.36 -1.18 -2.36 7.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.271 r_dihedral_angle_3_deg 15.284 r_dihedral_angle_4_deg 13.937 r_dihedral_angle_1_deg 5.312 r_long_range_B_refined 2.149 r_long_range_B_other 2.149 r_angle_refined_deg 1.133 r_angle_other_deg 1.062 r_mcangle_it 0.977 r_mcangle_other 0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.271 r_dihedral_angle_3_deg 15.284 r_dihedral_angle_4_deg 13.937 r_dihedral_angle_1_deg 5.312 r_long_range_B_refined 2.149 r_long_range_B_other 2.149 r_angle_refined_deg 1.133 r_angle_other_deg 1.062 r_mcangle_it 0.977 r_mcangle_other 0.977 r_scangle_other 0.886 r_mcbond_it 0.547 r_mcbond_other 0.547 r_scbond_it 0.482 r_scbond_other 0.482 r_chiral_restr 0.039 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 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 17470 Nucleic Acid Atoms 1064 Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing