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Crystal structure of chicken LGP2 with 5'ppp 10-mer dsRNA and ADP-AlF4-Mg2+ at 2.2 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JAJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 chLGP2, directly after size exclusion chromatography, was mixed with dsRNA in a 1:1 ratio and incubated for 30 minutes on ice. The complex was concentrated with an Amicon Ultra concentrator to around 10 mg/ml and then 2 mM ADP:AlF4 and 2 mM MgCl2 were added. 5 prime triphosphate 10-mer dsRNA:ADP:AlF4 complex was mixed with reservoir buffer (0.1 M Mg formate, 20% PEG3350M) in a 2:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.47 50.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.14 α = 90 b = 96.58 β = 90 c = 122.86 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 PILATUS3 6M 2014-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 75.93 99.9 0.169 8.73 6.64 43057
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 99.4 0.835 1.87 6.5
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 (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 5JAJ 2.2 75.93 40943 2114 99.91 0.1909 0.18818 0.1942 0.24457 0.2473 RANDOM 33.565
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] 1.37 -0.17 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.402 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 15.072 r_long_range_B_refined 6.333 r_long_range_B_other 6.274 r_dihedral_angle_1_deg 6.124 r_scangle_other 3.708 r_mcangle_it 3.316 r_mcangle_other 3.316 r_scbond_other 2.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.402 r_dihedral_angle_4_deg 17.321 r_dihedral_angle_3_deg 15.072 r_long_range_B_refined 6.333 r_long_range_B_other 6.274 r_dihedral_angle_1_deg 6.124 r_scangle_other 3.708 r_mcangle_it 3.316 r_mcangle_other 3.316 r_scbond_other 2.127 r_scbond_it 2.126 r_mcbond_it 1.926 r_mcbond_other 1.926 r_angle_refined_deg 1.365 r_angle_other_deg 0.959 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 5364 Nucleic Acid Atoms 464 Solvent Atoms 344 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing