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Structure of chicken LGP2 bound to 10-mer RNA mismatched duplex that mimics the influenza B virus vRNA promoter (panhandle) and to ADP-AlF4-Mg.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 Directly after size exclusion chromatography, chLGP2 was mixed with duplex RNA in a 1:1 ratio and incubated for 30 minutes on ice. The complexes were concentrated to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added.
The complex was mixed with reservoir solution (0.1M Na citrate pH 6.1
0.46 M NH4 dihydrophosphate)
in a ratio 1:2.
Crystal Properties Matthews coefficient Solvent content 2.47 50.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.9 α = 90 b = 96.462 β = 90 c = 122.324 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 2014-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97924 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 1.436 75.744 78.1 0.052 0.997 11.2 3.8 117940
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 1.436 1.557 18.2 0.719 0.673 1.6 4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.436 75.744 117939 5833 78.118 0.149 0.1478 0.148 0.1785 0.1783 22.583
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] -0.968 -0.219 1.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 17.823 r_dihedral_angle_6_deg 14.058 r_lrange_it 13.466 r_lrange_other 11.822 r_dihedral_angle_3_deg 11.621 r_scangle_it 6.309 r_scangle_other 6.309 r_dihedral_angle_1_deg 6.134 r_mcangle_it 5.663 r_mcangle_other 5.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 17.823 r_dihedral_angle_6_deg 14.058 r_lrange_it 13.466 r_lrange_other 11.822 r_dihedral_angle_3_deg 11.621 r_scangle_it 6.309 r_scangle_other 6.309 r_dihedral_angle_1_deg 6.134 r_mcangle_it 5.663 r_mcangle_other 5.662 r_dihedral_angle_2_deg 4.904 r_scbond_it 3.958 r_scbond_other 3.958 r_mcbond_it 3.438 r_mcbond_other 3.437 r_rigid_bond_restr 1.809 r_angle_refined_deg 1.242 r_angle_other_deg 0.452 r_dihedral_angle_other_2_deg 0.399 r_symmetry_nbd_refined 0.317 r_nbd_refined 0.249 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.169 r_nbd_other 0.152 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.062 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5294 Nucleic Acid Atoms 420 Solvent Atoms 714 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing