5E7K

Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WQ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293PEG 20000, PEG 550mme, KSCN, Tris-OAc
Crystal Properties
Matthews coefficientSolvent content
3.2462.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 209.5α = 90
b = 450.1β = 90
c = 621.6γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.00SLSX06SA

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
13.22001000.37537.7108.7955810-3102.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.31004.2974.3521.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4WQ13.2173.7191.34955729199999.990.19160.19140.2579107.4619
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_d18.789
f_angle_d1.67
f_chiral_restr0.068
f_bond_d0.01
f_plane_restr0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms89071
Nucleic Acid Atoms202855
Solvent Atoms
Heterogen Atoms2521

Software

Software
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction