1N32

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


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

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 = 400.3 α = 90
b = 400.3 β = 90
c = 175.48 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 90
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2001-05-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 -- ESRF ID14-4

Data Collection

Overall
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
2.99 141.42 95.5 -- 0.128 -- 3.52 -- 272610 -- -- 75.175
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)
3.0 3.11 80.1 -- 0.564 2.0 2.91 --

Refinement

Statistics
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 3.0 141.42 -- -- -- 258651 13151 91.9 -- 0.227 0.227 0.27 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 3.0 3.11 -- 1119 20326 0.3501 0.3638 -- 77.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 70.51
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.56
c_bond_d 0.006
c_angle_deg 1.21
c_dihedral_angle_d 28.45
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.56
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.56
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19170
Nucleic Acid Atoms 32903
Heterogen Atoms 202
Solvent Atoms 0

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection