4V57

Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin.


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
3.4163.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 208.848α = 90
b = 379.202β = 90
c = 739.283γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 3152006-03-05MSINGLE 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
13.518272.10.1048.63.3521699
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)
13.53.8513.90.411.91.1

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, 2AWB3.570731327521145252740.2640.30674.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
bond angles0.895
bond length0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18536
Nucleic Acid Atoms32831
Solvent Atoms300
Heterogen Atoms125

Software

Software
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing