2CWO

Crystal structure of RNA silencing suppressor p21 from Beet Yellows Virus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72930.2M K/Na Tartrate, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.5565

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 199.633α = 90
b = 199.633β = 90
c = 56.122γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

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
13.32098.820.1121.611.31949119263-3
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)
13.33.4295.80.6631912

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRTHROUGHOUT3.320184421822494398.820.211680.211680.210040.24443RANDOM132.327
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]
-2.79-1.4-2.794.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.517
r_dihedral_angle_3_deg22.368
r_dihedral_angle_4_deg20.655
r_dihedral_angle_1_deg6.244
r_scangle_it2.501
r_angle_refined_deg1.812
r_scbond_it1.439
r_mcangle_it0.764
r_mcbond_it0.428
r_symmetry_vdw_refined0.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.517
r_dihedral_angle_3_deg22.368
r_dihedral_angle_4_deg20.655
r_dihedral_angle_1_deg6.244
r_scangle_it2.501
r_angle_refined_deg1.812
r_scbond_it1.439
r_mcangle_it0.764
r_mcbond_it0.428
r_symmetry_vdw_refined0.374
r_nbtor_refined0.33
r_nbd_refined0.272
r_xyhbond_nbd_refined0.158
r_chiral_restr0.123
r_symmetry_hbond_refined0.071
r_bond_refined_d0.019
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5388
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing