3T1H

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (HASL) of transfer RNA lysine 3 (tRNALys3) bound to an mRNA with an AAA-codon in the A-site and 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, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.3 α = 90
b = 402.3 β = 90
c = 175.25 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2005-01-01
Diffraction Radiation
Monochromator Protocol
Si111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 0.97 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
3.1 50 98.0 -- -- -- -- 257375 252120 -- 2.0 --

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
MOLECULAR REPLACEMENT 3.11 29.72 -- 0.0 -- 252120 12418 99.0 -- -- 0.247 0.276 Same set as in 1J5E extended
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 3.11 3.29 -- 1970 37597 0.357 0.38 0.009 93.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 68.938
Anisotropic B[1][1] -6.5
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -6.5
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.01
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_dihedral_angle_d 19.6
c_improper_angle_d 1.64
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.43
Luzzati Sigma A (Observed) 0.75
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.79
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19229
Nucleic Acid Atoms 32829
Heterogen Atoms 229
Solvent Atoms 0

Software

Software
Software Name Purpose
CNS refinement version: 1.3
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data reduction
HKL-2000 data scaling
CNS phasing