7JJU

Crystal structure of en exoribonuclease-resistant RNA (xrRNA) from Potato leafroll virus (PLRV)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931 microL RNA solution (5 mg/mL RNA in 30 mM HEPES pH 7.5, 20 mM MgCl2, 100 mM KCl) + 1 microL crystallization solution (10% 2-methyl-2,4-pentanediol, 40 mM Sodium Cacodylate (pH 6.0), 12 mM Spermine, 150 mM KCl, 100 mM Guanidinium HCl) over a reservoir of 500 microL of 30% 2-methyl-2,4-pentanediol and 100mM Guanidinium HCl.
Crystal Properties
Matthews coefficientSolvent content
2.6152.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.19α = 90
b = 72.19β = 90
c = 137.14γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CMOSRDI CMOS_8M2019-09-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.20.9234ALS4.2.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.60449.7299.640.099560.10080.01561130.8641.31168963.33
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.6042.69799.561.6631.6850.9142.5338

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.60449.721.3511669109799.660.22610.22460.253462.95
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.5962
f_angle_d0.4406
f_chiral_restr0.0202
f_plane_restr0.0018
f_bond_d0.0012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms
Nucleic Acid Atoms2162
Solvent Atoms
Heterogen Atoms178

Software

Software
Software NamePurpose
XDSdata processing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing