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Crystal structure of chicken LGP2 with 5'ppp 26-mer hairpin RNA with 3' GG overhang and ADP-AlF4-Mg2+ at 2.0 A resolution.
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, SITTING DROP 5 277 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, 3 prime GG overhang 26-mer hairpin RNA:ADP:AlF4 complex was mixed with reservoir buffer containing 0.1 M citric acid pH 5.0, 0.8 M ammonium sulphate in a 1:1 ratio.
Crystal Properties Matthews coefficient Solvent content 2.43 49.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.86 α = 90 b = 97.43 β = 90 c = 122.58 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 2015-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
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 76.27 99.9 0.259 6.31 4.47 56661
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 2.1 98.7 0.795 1.38 4.35
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 5JB2 2 76.27 53847 2814 98.95 0.21945 0.21758 0.2226 0.255 0.2596 RANDOM 38.664
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] 2.5 -0.76 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.751 r_dihedral_angle_4_deg 16.982 r_dihedral_angle_3_deg 14.289 r_long_range_B_refined 6.437 r_long_range_B_other 6.181 r_dihedral_angle_1_deg 5.845 r_scangle_other 3.527 r_mcangle_it 3.286 r_mcangle_other 3.286 r_scbond_it 2.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.751 r_dihedral_angle_4_deg 16.982 r_dihedral_angle_3_deg 14.289 r_long_range_B_refined 6.437 r_long_range_B_other 6.181 r_dihedral_angle_1_deg 5.845 r_scangle_other 3.527 r_mcangle_it 3.286 r_mcangle_other 3.286 r_scbond_it 2.1 r_scbond_other 2.091 r_mcbond_it 1.995 r_mcbond_other 1.989 r_angle_refined_deg 1.278 r_angle_other_deg 0.93 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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 5290 Nucleic Acid Atoms 506 Solvent Atoms 268 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing