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Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 FluPolB PA mutant K135A at 9 mg per ml was mixed with 40 microM of nucleotides 1-13 vRNA 5prime end, 5-pAGUAGUAACAAGA-3, and 1.8 mM 28-mer CTD peptide, YSPTpSPS x 4 in a buffer containing 50 mM HEPES pH 7.5, 500 mM NaCl, 5% glycerol, 2 mM TCEP. Hanging drops for crystallization were set up at 20 C.
Crystal Properties Matthews coefficient Solvent content 3.1 60.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.93 α = 90 b = 202.269 β = 110.538 c = 135.733 γ = 90
Symmetry Space Group P 1 21 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 2017-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.25422 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 2.418 127.106 61.4 0.112 0.136 0.992 7.7 3 154519
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 2.42 2.69 64 0.618 0.769 0.63 1.9 2.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5FMZ 2.418 127.106 154519 7573 61.415 0.225 0.2233 0.2242 0.2567 0.2561 54.204
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] -0.034 0.054 0.129 -0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_3_deg 16.749 r_dihedral_angle_1_deg 5.258 r_lrange_it 4.204 r_lrange_other 4.204 r_mcangle_it 2.328 r_mcangle_other 2.328 r_scangle_it 1.888 r_scangle_other 1.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.528 r_dihedral_angle_4_deg 17.463 r_dihedral_angle_3_deg 16.749 r_dihedral_angle_1_deg 5.258 r_lrange_it 4.204 r_lrange_other 4.204 r_mcangle_it 2.328 r_mcangle_other 2.328 r_scangle_it 1.888 r_scangle_other 1.888 r_mcbond_it 1.303 r_mcbond_other 1.303 r_angle_refined_deg 1.197 r_angle_other_deg 1.056 r_scbond_it 1.03 r_scbond_other 1.03 r_symmetry_nbd_refined 0.228 r_ext_dist_refined_d 0.218 r_nbd_other 0.176 r_nbd_refined 0.172 r_symmetry_nbd_other 0.163 r_symmetry_xyhbond_nbd_refined 0.158 r_nbtor_refined 0.15 r_xyhbond_nbd_refined 0.138 r_ncsr_local_group_5 0.088 r_ncsr_local_group_3 0.085 r_ncsr_local_group_1 0.074 r_symmetry_nbtor_other 0.072 r_ncsr_local_group_2 0.064 r_chiral_restr 0.046 r_ncsr_local_group_4 0.016 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 35189 Nucleic Acid Atoms 532 Solvent Atoms 206 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing