5IB8

Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.0
Details PEG 20000, PEG 550mme, KSCN, Tris-OAc

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 209.15 α = 90
b = 448.16 β = 90
c = 617.8 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 -- 2015-09-06
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
3.13 154.45 100.0 0.419 -- -- 133.67 -- 1008570 -- -3.0 99.68
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)
3.13 3.21 100.0 4.322 -- 0.97 -- --

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 3.13 154.45 -- 1.33 -- 1008227 1998 99.95 -- 0.1921 0.192 0.2437 --
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 3.13 3.2083 -- 141 71295 0.3197 0.3481 -- 100.0
X Ray Diffraction 3.2083 3.295 -- 141 71446 0.2677 0.3062 -- 100.0
X Ray Diffraction 3.295 3.392 -- 143 71459 0.2494 0.3143 -- 100.0
X Ray Diffraction 3.392 3.5015 -- 142 71569 0.2404 0.2803 -- 100.0
X Ray Diffraction 3.5015 3.6266 -- 142 71497 0.2208 0.2768 -- 100.0
X Ray Diffraction 3.6266 3.7719 -- 142 71560 0.2045 0.2694 -- 100.0
X Ray Diffraction 3.7719 3.9435 -- 143 71676 0.1906 0.2378 -- 100.0
X Ray Diffraction 3.9435 4.1515 -- 142 71712 0.1845 0.2465 -- 100.0
X Ray Diffraction 4.1515 4.4116 -- 143 71773 0.1772 0.2281 -- 100.0
X Ray Diffraction 4.4116 4.7522 -- 143 71920 0.1734 0.2167 -- 100.0
X Ray Diffraction 4.7522 5.2305 -- 143 71974 0.1753 0.2361 -- 100.0
X Ray Diffraction 5.2305 5.9874 -- 144 72164 0.1751 0.2545 -- 100.0
X Ray Diffraction 5.9874 7.5435 -- 144 72484 0.1875 0.2484 -- 100.0
X Ray Diffraction 7.5435 154.638 -- 145 73700 0.1786 0.2074 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 109.663
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 18.286
f_plane_restr 0.008
f_chiral_restr 0.061
f_angle_d 1.491
f_bond_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 89757
Nucleic Acid Atoms 201873
Heterogen Atoms 5370
Solvent Atoms 0

Software

Software
Software Name Purpose
XSCALE data scaling
PHASER phasing
PHENIX refinement
PDB_EXTRACT data extraction version: 3.20
XDS data reduction