4V5R

The crystal structure of EF-Tu and Trp-tRNA-Trp bound to a cognate codon on the 70S ribosome.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WRNPDB ENTRY 2WRN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.3100 MM MES PH 6.3, 60-100 MM KCL, 50 MM SUCROSE, 1% GLYCEROL, 5.2% (W/V) PEG20K
Crystal Properties
Matthews coefficientSolvent content
3.3863.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 290.2α = 90
b = 269.2β = 91.54
c = 404γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2010-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
13.15099.80.027.126.311166061.2470.8
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)
13.13.299.91.151.245.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WRN3.15011166065566699.80.23740.23740.2637INHERITED FROM 2WRN100.8
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]
2.78-12.53-1.82-0.96
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29
c_improper_angle_d1.54
c_angle_deg1.2
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29
c_improper_angle_d1.54
c_angle_deg1.2
c_bond_d0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22130
Nucleic Acid Atoms37696
Solvent Atoms
Heterogen Atoms89

Software

Software
Software NamePurpose
CNSmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing