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Crystal structure of chicken LGP2 with 5'p 12-mer dsRNA at 3.6 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 6.5 277 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. chLGP2:12bp dsRNA:ADP:AlF4 complex was mixed with reservoir buffer (0.1 M Bis-Tris propane pH 6.5, 0.05-0.1 M magnesium formate) in a 2:1 ratio
Crystal Properties Matthews coefficient Solvent content 2.71 54.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.09 α = 90 b = 90.09 β = 90 c = 196.73 γ = 120
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 2014-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9786 ESRF ID23-1
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 3.58 78.02 78.02 0.067 20.74 11.51 10663
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 3.58 3.73 99 1.18 10.32
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 3.58 78.02 10121 542 99.83 0.25647 0.25312 0.2548 0.31881 0.2516 RANDOM 202.316
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] 0.43 0.22 0.43 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.078 r_dihedral_angle_3_deg 11.876 r_long_range_B_refined 11.442 r_long_range_B_other 11.441 r_dihedral_angle_4_deg 11.038 r_mcangle_it 7.897 r_mcangle_other 7.896 r_scangle_other 6.344 r_dihedral_angle_1_deg 5.159 r_mcbond_it 4.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.078 r_dihedral_angle_3_deg 11.876 r_long_range_B_refined 11.442 r_long_range_B_other 11.441 r_dihedral_angle_4_deg 11.038 r_mcangle_it 7.897 r_mcangle_other 7.896 r_scangle_other 6.344 r_dihedral_angle_1_deg 5.159 r_mcbond_it 4.585 r_mcbond_other 4.585 r_scbond_it 3.612 r_scbond_other 3.608 r_angle_refined_deg 0.954 r_angle_other_deg 0.857 r_chiral_restr 0.055 r_bond_refined_d 0.006 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 5007 Nucleic Acid Atoms 512 Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing