4V9J

70S ribosome translocation intermediate GDPNP-II containing elongation factor EFG/GDPNP, mRNA, and tRNA bound in the pe*/E state.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F1EPDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ
experimental modelPDB 3F1FPDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ
experimental modelPDB 2WRIPDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ
experimental modelPDB 2WRJPDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12.9% PEG20000, 2.8% PPG P400, 5.1% PEG550 MME, 200 mM potassium thiocyanate, Tris acetate
Crystal Properties
Matthews coefficientSolvent content
4.0469.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 302.3911α = 90
b = 683.9183β = 89.9983
c = 356.6977γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-06-07MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 315r2012-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03322APS23-ID-D
2SYNCHROTRONALS BEAMLINE 12.3.11.116ALS12.3.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
1,23.8640960.3365.13.846244621.5

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRIES 3F1E, 3F1F, 2WRI, AND 2WRJ3.86402462446216180.2640.2640.3166RANDOM
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
o_angle_deg1.101
o_bond_d0.022
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24442
Nucleic Acid Atoms34502
Solvent Atoms
Heterogen Atoms33

Software

Software
Software NamePurpose
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
SCALAdata scaling