1N34

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position


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 = 401.84 α = 90
b = 401.84 β = 90
c = 173.85 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
3.78 141.42 96.1 -- 0.081 -- 3.4 -- 135995 -- -- 72.99
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)
3.78 3.94 99.3 -- 0.295 1.7 -- --

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 3.8 141.42 -- -- -- 128977 6381 92.6 -- 0.241 0.241 0.312 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 3.8 3.94 -- 597 11813 0.2876 0.3528 -- 90.12
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 97.68
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.53
c_bond_d 0.007
c_angle_deg 1.24
c_dihedral_angle_d 28.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.45
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.61
Luzzati Sigma A (R-Free Set) 0.69
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19170
Nucleic Acid Atoms 32585
Heterogen Atoms 2
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