5EL7

Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 293.0
Details PEG 20000, PEG 550mme, KSCN, Tris-OAc

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 209.7 α = 90
b = 449.5 β = 90
c = 620.3 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-11-02
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.00 SLS X06SA

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
3.05 175 100.0 0.302 -- -- 75.2 -- 1099625 -- -3.0 92.12
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)
3.05 3.15 100.0 5.075 -- 1.0 -- --

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 3.15 152.167 -- 1.33 -- 998508 2000 99.92 -- 0.1917 0.1916 0.2475 --
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 3.15 3.2288 -- 142 70806 0.33 0.3823 -- 100.0
X Ray Diffraction 3.2288 3.3161 -- 142 70702 0.3024 0.3598 -- 100.0
X Ray Diffraction 3.3161 3.4137 -- 142 70703 0.2797 0.3333 -- 100.0
X Ray Diffraction 3.4137 3.5239 -- 142 70849 0.2538 0.3186 -- 100.0
X Ray Diffraction 3.5239 3.6498 -- 142 70866 0.2312 0.2957 -- 100.0
X Ray Diffraction 3.6498 3.796 -- 142 70935 0.2126 0.2828 -- 100.0
X Ray Diffraction 3.796 3.9687 -- 143 70968 0.1976 0.2687 -- 100.0
X Ray Diffraction 3.9687 4.178 -- 142 70954 0.179 0.2692 -- 100.0
X Ray Diffraction 4.178 4.4398 -- 143 71061 0.1665 0.2131 -- 100.0
X Ray Diffraction 4.4398 4.7826 -- 143 71173 0.158 0.233 -- 100.0
X Ray Diffraction 4.7826 5.2639 -- 143 71267 0.1533 0.2041 -- 100.0
X Ray Diffraction 5.2639 6.0256 -- 144 71463 0.1552 0.1868 -- 100.0
X Ray Diffraction 6.0256 7.5917 -- 144 71810 0.1812 0.2372 -- 100.0
X Ray Diffraction 7.5917 152.345 -- 146 72951 0.1826 0.2313 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 102.381
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 19.257
f_angle_d 1.842
f_chiral_restr 0.072
f_bond_d 0.011
f_plane_restr 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 89067
Nucleic Acid Atoms 202817
Heterogen Atoms 4302
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHENIX refinement
PDB_EXTRACT data extraction version: 3.15
XDS data reduction
PHASER phasing