6TY0

NT PART CRYSTAL STRUCTURE OF THE RYMV-ENCODED VIRAL RNA SILENCING SUPPRESSOR P1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIQUID DIFFUSION29320 mM Tris pH 8, 75 mM NaCl, 1 mM DTT and 300 mM ZnCl2
Crystal Properties
Matthews coefficientSolvent content
3.5564

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 195.612α = 90
b = 195.612β = 90
c = 195.612γ = 90
Symmetry
Space GroupF 41 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2013-02-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

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
12112.941000.0550.0580.0120.999452022243
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)
122.111000.886

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.1112.941839587899.970.185640.184230.21417RANDOM44.583
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
r_dihedral_angle_2_deg35.511
r_dihedral_angle_3_deg16.691
r_dihedral_angle_4_deg15.709
r_long_range_B_refined10.078
r_long_range_B_other9.89
r_scangle_other7.108
r_dihedral_angle_1_deg6.397
r_mcangle_other4.814
r_mcangle_it4.812
r_scbond_it4.599
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.511
r_dihedral_angle_3_deg16.691
r_dihedral_angle_4_deg15.709
r_long_range_B_refined10.078
r_long_range_B_other9.89
r_scangle_other7.108
r_dihedral_angle_1_deg6.397
r_mcangle_other4.814
r_mcangle_it4.812
r_scbond_it4.599
r_scbond_other4.599
r_mcbond_it3.487
r_mcbond_other3.466
r_angle_refined_deg1.709
r_angle_other_deg0.786
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms1545
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
HKL2Mapphasing