Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin

X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help


Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, NH4Cl, KCl, CaCl2, magnesium acetate, potassium-MES, sodium cacodylate, PH 6.5, VAPOR DIFFUSION, HANGING DROP AT 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 401.6 α = 90
b = 401.6 β = 90
c = 176.02 γ = 90
Space Group P 41 21 2


Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-06-24
Diffraction Radiation
Monochromator Protocol
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline

Data Collection

Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
3.35 74.54 92.2 -- 0.161 -- 4.65 -- 188834 -- -- 76.56
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
3.35 3.47 79.4 -- 0.586 2.1 -- --


Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
DIFFERENCE FOURIER 3.35 74.54 -- -- -- 181372 9128 88.6 -- 0.2251 0.225 0.284 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 3.35 3.47 -- 740 13619 0.311 0.3481 -- 70.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 93.88
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_angle_deg 1.22
c_improper_angle_d 1.57
c_dihedral_angle_d 28.38
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.41
Luzzati Sigma A (Observed) 0.58
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.63
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19170
Nucleic Acid Atoms 32820
Heterogen Atoms 150
Solvent Atoms 0


Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
CNS refinement
CNS phasing