4GKJ

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUG-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, temperature 277.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 400.55 α = 90
b = 400.55 β = 90
c = 176.19 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 -- 2010-08-17
Diffraction Radiation
Monochromator Protocol
Silicon SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97 APS 24-ID-C

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
3 283 62.3 -- -- -- -- -- 276947 -- -3.0 --
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)
2.9 3.04 98.1 9.636 -- 0.21 -- --

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 3.298 97.148 -- 0.92 -- 207838 10445 97.34 -- 0.19 0.1884 0.2216 --
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 3.298 3.3355 -- 305 6022 0.3227 0.3387 -- 89.0
X Ray Diffraction 3.3355 3.3747 -- 369 6620 0.2941 0.3308 -- 100.0
X Ray Diffraction 3.3747 3.4159 -- 343 6675 0.2781 0.2985 -- 100.0
X Ray Diffraction 3.4159 3.4591 -- 344 6699 0.2701 0.3002 -- 100.0
X Ray Diffraction 3.4591 3.5047 -- 374 6632 0.2645 0.3024 -- 100.0
X Ray Diffraction 3.5047 3.5527 -- 348 6704 0.2487 0.2832 -- 100.0
X Ray Diffraction 3.5527 3.6034 -- 351 6691 0.2353 0.2581 -- 100.0
X Ray Diffraction 3.6034 3.6572 -- 360 6652 0.2232 0.2448 -- 100.0
X Ray Diffraction 3.6572 3.7144 -- 331 6682 0.2183 0.2492 -- 99.0
X Ray Diffraction 3.7144 3.7753 -- 345 6667 0.2059 0.2357 -- 99.0
X Ray Diffraction 3.7753 3.8404 -- 335 6691 0.2006 0.2299 -- 99.0
X Ray Diffraction 3.8404 3.9102 -- 381 6622 0.1923 0.2318 -- 99.0
X Ray Diffraction 3.9102 3.9854 -- 338 6671 0.1834 0.2311 -- 99.0
X Ray Diffraction 3.9854 4.0668 -- 401 6594 0.1809 0.2301 -- 99.0
X Ray Diffraction 4.0668 4.1552 -- 348 6639 0.1685 0.2086 -- 99.0
X Ray Diffraction 4.1552 4.2519 -- 369 6666 0.1668 0.2161 -- 99.0
X Ray Diffraction 4.2519 4.3582 -- 335 6668 0.1712 0.2035 -- 99.0
X Ray Diffraction 4.3582 4.476 -- 373 6641 0.1669 0.2021 -- 99.0
X Ray Diffraction 4.476 4.6077 -- 307 6687 0.1619 0.2013 -- 98.0
X Ray Diffraction 4.6077 4.7564 -- 356 6645 0.1578 0.1814 -- 99.0
X Ray Diffraction 4.7564 4.9264 -- 338 6612 0.1527 0.1898 -- 98.0
X Ray Diffraction 4.9264 5.1237 -- 380 6593 0.15 0.1928 -- 98.0
X Ray Diffraction 5.1237 5.3568 -- 351 6617 0.1435 0.1909 -- 98.0
X Ray Diffraction 5.3568 5.6392 -- 337 6597 0.1471 0.1945 -- 97.0
X Ray Diffraction 5.6392 5.9925 -- 362 6584 0.1503 0.2007 -- 97.0
X Ray Diffraction 5.9925 6.4551 -- 344 6550 0.1584 0.2061 -- 96.0
X Ray Diffraction 6.4551 7.1045 -- 341 6491 0.1562 0.1962 -- 95.0
X Ray Diffraction 7.1045 8.1321 -- 349 6414 0.1555 0.1869 -- 93.0
X Ray Diffraction 8.1321 10.2439 -- 330 6315 0.1843 0.2206 -- 91.0
X Ray Diffraction 10.2439 97.1898 -- 300 6052 0.2574 0.2506 -- 83.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 92.8082
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.069
f_dihedral_angle_d 18.343
f_angle_d 1.354
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19231
Nucleic Acid Atoms 32766
Heterogen Atoms 230
Solvent Atoms 0

Software

Computing
Computing Package Purpose
Console Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX Structure Solution
PHENIX (phenix.refine: 1.8_1069) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
phenix refinement
Xscale data reduction