4V5P

The crystal structure of EF-Tu and A9C-tRNA-Trp bound to a near- 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
3.3763.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 289.9α = 90
b = 268.5β = 91.62
c = 403.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC2010-04-01MSINGLE 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
13.15097.90.0210.48510906961.752.2
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)
13.13.293.21.031.694.4

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 2WRN3.150109069654315980.2430.2430.267INHERITED FROM 2WRN77.9
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]
5.25-10.64-0.84-4.41
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d29
c_improper_angle_d1.51
c_angle_deg1.2
c_bond_d0.007
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_d1.51
c_angle_deg1.2
c_bond_d0.007
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 Atoms22129
Nucleic Acid Atoms37693
Solvent Atoms
Heterogen Atoms89

Software

Software
Software NamePurpose
CNSmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing