4DR4

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, cognate transfer RNA anticodon stem-loop and multiple copies of paromomycin molecules bound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1HANGING DROP6.5277MPD, pH 6.5, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
4.572.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 400.951α = 90
b = 400.951β = 90
c = 176.675γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.98APS24-ID-C

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
13.969501000.2533.97.3123861123861-3-3
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)
13.9694.041000.9926.76102

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESIS3.96949.7321.34123736123736618799.940.15610.15310.2124FROM PDB ENTRY 2VQE101.1617
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]
-12.2147-12.21472.7328
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d26.098
f_angle_d1.527
f_chiral_restr0.083
f_bond_d0.013
f_plane_restr0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19152
Nucleic Acid Atoms32880
Solvent Atoms498
Heterogen Atoms1115

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing