☰ Navigation Tabs
Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WSB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 281 Bat influenza polymerase protein in 50 mM HEPES-NaOH, 500 mM NaCl, 5 % glycerol, 2 mM TCEP, pH = 7.5 was adjusted to a concentration of 10 mg per ml, mixed in a 1:1 ratio with vRNA, which was an equimolar mixture of nucleotides 1-16 from the 5 prime end and nucleotides 1-18 or 3-18 from the 3 prime end. Protein-RNA with the addition of 5 mM m7GTP was mixed with mother liquor containing 0.7-1.5 M sodium-potassium phosphate at pH 5.0
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 269.34 α = 90 b = 148.7 β = 98.17 c = 88.51 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 2014-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.979 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.9 50 99.6 0.102 0.115 0.998 10.75 4.63 76144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.98 99.8 1.22 1.38 0.597 1.08 4.65
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 4WSB 2.9 50 72389 3755 99.58 0.23592 0.23399 0.2358 0.27294 0.27 RANDOM 115.697
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] 2.15 5.88 -1.05 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_4_deg 12.907 r_long_range_B_refined 10.233 r_long_range_B_other 10.226 r_mcangle_it 6.322 r_mcangle_other 6.322 r_dihedral_angle_1_deg 6.151 r_scangle_other 5.847 r_mcbond_it 3.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.778 r_dihedral_angle_3_deg 15.486 r_dihedral_angle_4_deg 12.907 r_long_range_B_refined 10.233 r_long_range_B_other 10.226 r_mcangle_it 6.322 r_mcangle_other 6.322 r_dihedral_angle_1_deg 6.151 r_scangle_other 5.847 r_mcbond_it 3.789 r_mcbond_other 3.786 r_scbond_it 3.36 r_scbond_other 3.339 r_angle_refined_deg 1.139 r_angle_other_deg 0.906 r_chiral_restr 0.063 r_bond_refined_d 0.008 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 17434 Nucleic Acid Atoms 600 Solvent Atoms 38 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing