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Influenza B polymerase bound to vRNA promoter and capped RNA primer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WRT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 277 35 microM of FluB polymerase was mixed with 40 microM of the vRNA promoter and 40 microM 13-mer capped RNA primer in a buffer containing 500 mM NaCl, 50 mM HEPES pH 7.5, 5% glycerol and 2 mM TCEP. The best diffracting crystals appeared in 100 mM sodium acetate pH 3.8 - 4.0 and 150 mM di-ammonium phosphate
Crystal Properties Matthews coefficient Solvent content 5.32 76.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 200.41 α = 90 b = 200.41 β = 90 c = 254.61 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 2015-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.2724 ESRF ID23-1
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 3.8 173.56 99.9 0.411 0.999 9.76 46.4 58685
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 3.8 4 100 2.743 0.72 1.2 4.1
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 4WRT 3.8 173.56 55900 2785 99.9 0.23631 0.23471 0.2359 0.26745 0.2645 RANDOM 172.682
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] -6.58 -3.29 -6.58 21.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_4_deg 12.178 r_long_range_B_refined 8.172 r_long_range_B_other 8.172 r_mcangle_other 5.213 r_mcangle_it 5.212 r_dihedral_angle_1_deg 5.121 r_scangle_other 4.389 r_mcbond_it 3.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.493 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_4_deg 12.178 r_long_range_B_refined 8.172 r_long_range_B_other 8.172 r_mcangle_other 5.213 r_mcangle_it 5.212 r_dihedral_angle_1_deg 5.121 r_scangle_other 4.389 r_mcbond_it 3.002 r_mcbond_other 2.997 r_scbond_it 2.373 r_scbond_other 2.373 r_angle_refined_deg 0.996 r_angle_other_deg 0.869 r_chiral_restr 0.054 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 17457 Nucleic Acid Atoms 769 Solvent Atoms Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing