4GKK

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 AUA-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 = 402.37 α = 90
b = 402.37 β = 90
c = 175.62 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 -- 2010-08-11
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
3.2 73.5 47.9 -- -- -- -- -- 230910 -- -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)
2.91 3.05 78.6 0.017 -- 0.15 -- --

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 3.2 73.466 -- 0.78 -- 230816 11785 98.3 -- 0.1973 0.1952 0.2359 --
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 3.2 3.2364 -- 370 7262 0.3296 0.3571 -- 99.0
X Ray Diffraction 3.2364 3.2744 -- 380 7315 0.3183 0.343 -- 99.0
X Ray Diffraction 3.2744 3.3144 -- 376 7312 0.3018 0.3474 -- 99.0
X Ray Diffraction 3.3144 3.3563 -- 371 7325 0.2956 0.3261 -- 99.0
X Ray Diffraction 3.3563 3.4005 -- 382 7323 0.2838 0.3155 -- 99.0
X Ray Diffraction 3.4005 3.4471 -- 418 7319 0.2672 0.3014 -- 99.0
X Ray Diffraction 3.4471 3.4963 -- 412 7249 0.2611 0.2973 -- 99.0
X Ray Diffraction 3.4963 3.5485 -- 430 7250 0.2565 0.292 -- 99.0
X Ray Diffraction 3.5485 3.604 -- 412 7325 0.2377 0.2847 -- 99.0
X Ray Diffraction 3.604 3.663 -- 395 7331 0.2264 0.2684 -- 99.0
X Ray Diffraction 3.663 3.7262 -- 434 7262 0.2207 0.2496 -- 99.0
X Ray Diffraction 3.7262 3.7939 -- 406 7276 0.1993 0.2506 -- 99.0
X Ray Diffraction 3.7939 3.8669 -- 382 7327 0.1901 0.2212 -- 99.0
X Ray Diffraction 3.8669 3.9458 -- 419 7264 0.1827 0.2324 -- 99.0
X Ray Diffraction 3.9458 4.0316 -- 388 7334 0.1788 0.2207 -- 99.0
X Ray Diffraction 4.0316 4.1254 -- 385 7341 0.18 0.2257 -- 99.0
X Ray Diffraction 4.1254 4.2286 -- 418 7291 0.1729 0.2101 -- 99.0
X Ray Diffraction 4.2286 4.3429 -- 372 7363 0.1625 0.2064 -- 99.0
X Ray Diffraction 4.3429 4.4707 -- 391 7350 0.164 0.214 -- 99.0
X Ray Diffraction 4.4707 4.6149 -- 391 7327 0.1617 0.203 -- 99.0
X Ray Diffraction 4.6149 4.7799 -- 393 7338 0.1624 0.1911 -- 99.0
X Ray Diffraction 4.7799 4.9712 -- 376 7357 0.1612 0.21 -- 99.0
X Ray Diffraction 4.9712 5.1974 -- 378 7358 0.1573 0.1971 -- 99.0
X Ray Diffraction 5.1974 5.4713 -- 415 7331 0.1528 0.2077 -- 98.0
X Ray Diffraction 5.4713 5.814 -- 388 7344 0.1576 0.2242 -- 98.0
X Ray Diffraction 5.814 6.2627 -- 347 7360 0.1637 0.2065 -- 98.0
X Ray Diffraction 6.2627 6.8925 -- 412 7281 0.1639 0.2155 -- 97.0
X Ray Diffraction 6.8925 7.8888 -- 372 7294 0.1596 0.2034 -- 96.0
X Ray Diffraction 7.8888 9.9352 -- 397 7219 0.1815 0.2225 -- 95.0
X Ray Diffraction 9.9352 73.485 -- 375 7003 0.2519 0.2672 -- 88.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 96.1629
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.068
f_dihedral_angle_d 18.427
f_angle_d 1.347
f_bond_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19231
Nucleic Acid Atoms 32727
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