5JB2

Crystal structure of chicken LGP2 with 5'ppp 10-mer dsRNA and ADP-AlF4-Mg2+ at 2.2 A resolution.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8277chLGP2, 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 coefficientSolvent content
2.4750.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.14α = 90
b = 96.58β = 90
c = 122.86γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-09-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.275.9399.90.1698.736.6443057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2899.40.8351.876.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5JAJ2.275.9340943211499.910.19090.188180.24457RANDOM33.565
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.402
r_dihedral_angle_4_deg17.321
r_dihedral_angle_3_deg15.072
r_long_range_B_refined6.333
r_long_range_B_other6.274
r_dihedral_angle_1_deg6.124
r_scangle_other3.708
r_mcangle_it3.316
r_mcangle_other3.316
r_scbond_other2.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.402
r_dihedral_angle_4_deg17.321
r_dihedral_angle_3_deg15.072
r_long_range_B_refined6.333
r_long_range_B_other6.274
r_dihedral_angle_1_deg6.124
r_scangle_other3.708
r_mcangle_it3.316
r_mcangle_other3.316
r_scbond_other2.127
r_scbond_it2.126
r_mcbond_it1.926
r_mcbond_other1.926
r_angle_refined_deg1.365
r_angle_other_deg0.959
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms5364
Nucleic Acid Atoms464
Solvent Atoms344
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing