4IFD | pdb_00004ifd

Crystal structure of an 11-subunit eukaryotic exosome complex bound to RNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2NN62NN6, 2WP8, 2JA9, 2JE6
experimental modelPDB 2WP82NN6, 2WP8, 2JA9, 2JE6
experimental modelPDB 2JA92NN6, 2WP8, 2JA9, 2JE6
experimental modelPDB 2JE62NN6, 2WP8, 2JA9, 2JE6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52920.02M Tris pH7.5, 0.05M NaCl, 0.001M MnCl2, 0.002M MgCl2, 1mM TCEP, 0.15M MES pH6.5, 0.27M NaBr, 11.4-12.2% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.6753.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 154.09α = 90
b = 107.44β = 110.63
c = 150.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2011-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9199SLSX10SA

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
12.80549.6487.40.17612.2512.89913799137-359.5
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)
12.8356.50.5481.892.511922

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2NN6, 2WP8, 2JA9, 2JE62.80549.6381.999913799101495687.860.18460.18460.18250.190.22390.23RANDOM
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_d9.903
f_angle_d0.542
f_chiral_restr0.035
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms25991
Nucleic Acid Atoms540
Solvent Atoms244
Heterogen Atoms54

Software

Software
Software NamePurpose
RemDAqdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling