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Replication-like initiation state of influenza polymerase with GTP and CTP at respectively the -1 and +1 positions (strain A/little yellow-shouldered bat/Guatemala/060/2010/H17N10)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9F2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 5 mg/ml polymerase with 5.1 mg/ml (19.5 microM) with 1.14 x molar excess of each RNA (v5' 1-16, v3' 1-18+3 and 15-mer capped primer, see Figure 1a) mixed in 1:1 ratio of 100 mM amino acids, 100 mM Tris/Bicine pH8.5, 8% ethylene glycol (v/v), 4% PEG 8000 (w/v) by hanging drop at room temperature. Soaking was performed with 5 mM GTP, 5 mM CTP and 5 mM MgCl2 for 5h.
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.937 α = 90 b = 119.005 β = 90 c = 251.381 γ = 90
Symmetry Space Group P 21 21 21
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 2020-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9795 Diamond I03
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 1.905 86.6 71.5 0.084 0.091 0.999 13.3 6.9 151625
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 1.91 2.11 0.955 1.04 0.708 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.905 86.566 151625 7590 71.224 0.191 0.1891 0.2315 0.2246 49.685
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] -0.165 0.223 -0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.745 r_dihedral_angle_6_deg 14.196 r_lrange_other 8.171 r_lrange_it 8.169 r_dihedral_angle_2_deg 7.499 r_dihedral_angle_1_deg 6.876 r_scangle_it 6.093 r_scangle_other 6.093 r_mcangle_it 5.509 r_mcangle_other 5.508
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.745 r_dihedral_angle_6_deg 14.196 r_lrange_other 8.171 r_lrange_it 8.169 r_dihedral_angle_2_deg 7.499 r_dihedral_angle_1_deg 6.876 r_scangle_it 6.093 r_scangle_other 6.093 r_mcangle_it 5.509 r_mcangle_other 5.508 r_scbond_it 3.876 r_scbond_other 3.876 r_mcbond_it 3.623 r_mcbond_other 3.623 r_angle_refined_deg 1.458 r_angle_other_deg 0.495 r_symmetry_xyhbond_nbd_refined 0.245 r_nbd_refined 0.219 r_dihedral_angle_other_2_deg 0.189 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.164 r_nbd_other 0.151 r_symmetry_nbd_refined 0.133 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.07 r_symmetry_xyhbond_nbd_other 0.02 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17411 Nucleic Acid Atoms 639 Solvent Atoms 700 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling