4DR6

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position and streptomycin bound


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 6.5
Temperature 277.0
Details MPD, pH 6.5, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 402.6 α = 90
b = 402.6 β = 90
c = 174.9 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
PIXEL DECTRIS PILATUS 6M -- 2011-06-28
Diffraction Radiation
Monochromator Protocol
double crystal Si(111) monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X25 1.1 NSLS X25

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
3.3 50 99.9 0.092 -- -- -- 213602 213602 -3.0 -3.0 104.363
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)
3.3 3.39 100.0 0.012 -- 2.02 -- --

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
FOURIER SYNTHESIS 3.3 49.484 -- 1.99 213574 213574 10749 99.97 -- 0.1554 0.1534 0.1918 FROM PDB ENTRY 2VQE
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 3.3 3.3374 -- 342 6618 0.2586 0.3135 -- 100.0
X Ray Diffraction 3.3374 3.3767 -- 384 6717 0.2393 0.2607 -- 100.0
X Ray Diffraction 3.3767 3.4178 -- 352 6670 0.2289 0.2847 -- 100.0
X Ray Diffraction 3.4178 3.4611 -- 339 6712 0.2159 0.248 -- 100.0
X Ray Diffraction 3.4611 3.5066 -- 366 6697 0.212 0.2459 -- 100.0
X Ray Diffraction 3.5066 3.5547 -- 352 6698 0.2087 0.2537 -- 100.0
X Ray Diffraction 3.5547 3.6054 -- 361 6667 0.2034 0.2505 -- 100.0
X Ray Diffraction 3.6054 3.6592 -- 383 6709 0.1867 0.2542 -- 100.0
X Ray Diffraction 3.6592 3.7164 -- 350 6700 0.1719 0.2108 -- 100.0
X Ray Diffraction 3.7164 3.7773 -- 361 6704 0.1636 0.1989 -- 100.0
X Ray Diffraction 3.7773 3.8424 -- 384 6678 0.1576 0.1944 -- 100.0
X Ray Diffraction 3.8424 3.9122 -- 356 6709 0.157 0.1947 -- 100.0
X Ray Diffraction 3.9122 3.9875 -- 340 6764 0.1519 0.1875 -- 100.0
X Ray Diffraction 3.9875 4.0688 -- 344 6731 0.1478 0.1917 -- 100.0
X Ray Diffraction 4.0688 4.1572 -- 345 6727 0.1436 0.2089 -- 100.0
X Ray Diffraction 4.1572 4.2539 -- 359 6735 0.14 0.1851 -- 100.0
X Ray Diffraction 4.2539 4.3602 -- 351 6718 0.1362 0.1843 -- 100.0
X Ray Diffraction 4.3602 4.478 -- 370 6770 0.1313 0.1744 -- 100.0
X Ray Diffraction 4.478 4.6097 -- 316 6777 0.1283 0.1828 -- 100.0
X Ray Diffraction 4.6097 4.7584 -- 352 6727 0.1278 0.1726 -- 100.0
X Ray Diffraction 4.7584 4.9283 -- 332 6793 0.1201 0.1738 -- 100.0
X Ray Diffraction 4.9283 5.1254 -- 341 6785 0.1232 0.1593 -- 100.0
X Ray Diffraction 5.1254 5.3584 -- 382 6749 0.1322 0.1712 -- 100.0
X Ray Diffraction 5.3584 5.6406 -- 342 6812 0.1254 0.1686 -- 100.0
X Ray Diffraction 5.6406 5.9934 -- 390 6785 0.1223 0.162 -- 100.0
X Ray Diffraction 5.9934 6.4552 -- 344 6839 0.1277 0.1814 -- 100.0
X Ray Diffraction 6.4552 7.1032 -- 347 6864 0.1249 0.164 -- 100.0
X Ray Diffraction 7.1032 8.1271 -- 370 6866 0.1264 0.1569 -- 100.0
X Ray Diffraction 8.1271 10.2244 -- 399 6933 0.1541 0.1869 -- 100.0
X Ray Diffraction 10.2244 49.4892 -- 395 7171 0.2062 0.2168 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 120.824
Anisotropic B[1][1] 2.4527
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.4527
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.6777
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 17.616
f_plane_restr 0.005
f_chiral_restr 0.065
f_angle_d 0.946
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19127
Nucleic Acid Atoms 33097
Heterogen Atoms 418
Solvent Atoms 907

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
xds Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
PHENIX (phenix.refine: dev_978) Structure Solution
PHENIX (phenix.refine: dev_978) Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
phenix refinement
Xscale data reduction