4V5Y

Crystal structure of the bacterial ribosome from Escherichia coli in complex with paromomycin and ribosome recycling factor (RRF).


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AVY2AVY,2AW4,2AW7,2AWB
experimental modelPDB 2AW42AVY,2AW4,2AW7,2AWB
experimental modelPDB 2AW72AVY,2AW4,2AW7,2AWB
experimental modelPDB 2AWB2AVY,2AW4,2AW7,2AWB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1batch7.5277MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.3763.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.873α = 90
b = 378.748β = 90
c = 738.261γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 3152007-03-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 12.3.11.111ALS12.3.1

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
14.456995.60.09611.73.5341454
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)
14.454.5391.90.49922.4

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2AVY,2AW4,2AW7,2AWB4.45403565093412101696795.70.2630.309
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
c_angle_deg0.94
c_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18536
Nucleic Acid Atoms32831
Solvent Atoms300
Heterogen Atoms102

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing