4DR7

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second 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 = 402.49 α = 90
b = 402.49 β = 90
c = 174.79 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
3.75 50 99.9 0.136 -- -- -- 146049 146049 -3.0 -3.0 121.622
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)
3.75 3.85 100.0 0.014 -- 1.99 -- --

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 3.75 48.909 -- 1.99 146005 146005 7300 99.94 -- 0.1507 0.1481 0.2008 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 3.75 3.7926 -- 237 4584 0.2365 0.2965 -- 100.0
X Ray Diffraction 3.7926 3.8372 -- 256 4543 0.235 0.2926 -- 100.0
X Ray Diffraction 3.8372 3.8839 -- 281 4552 0.231 0.2723 -- 100.0
X Ray Diffraction 3.8839 3.9331 -- 194 4570 0.2265 0.2823 -- 100.0
X Ray Diffraction 3.9331 3.9848 -- 251 4580 0.1972 0.2281 -- 100.0
X Ray Diffraction 3.9848 4.0394 -- 233 4587 0.1884 0.2796 -- 100.0
X Ray Diffraction 4.0394 4.0971 -- 228 4582 0.1756 0.2489 -- 100.0
X Ray Diffraction 4.0971 4.1582 -- 241 4596 0.1781 0.2498 -- 100.0
X Ray Diffraction 4.1582 4.2231 -- 249 4554 0.1697 0.2403 -- 100.0
X Ray Diffraction 4.2231 4.2923 -- 231 4594 0.1628 0.222 -- 100.0
X Ray Diffraction 4.2923 4.3663 -- 245 4593 0.149 0.2084 -- 100.0
X Ray Diffraction 4.3663 4.4456 -- 256 4544 0.1412 0.1973 -- 100.0
X Ray Diffraction 4.4456 4.5311 -- 209 4637 0.1323 0.1999 -- 100.0
X Ray Diffraction 4.5311 4.6235 -- 230 4620 0.131 0.2028 -- 100.0
X Ray Diffraction 4.6235 4.724 -- 243 4603 0.1283 0.2003 -- 100.0
X Ray Diffraction 4.724 4.8337 -- 244 4578 0.1211 0.1743 -- 100.0
X Ray Diffraction 4.8337 4.9545 -- 211 4633 0.1155 0.1891 -- 100.0
X Ray Diffraction 4.9545 5.0883 -- 238 4621 0.1151 0.1774 -- 100.0
X Ray Diffraction 5.0883 5.2379 -- 242 4607 0.1183 0.168 -- 100.0
X Ray Diffraction 5.2379 5.4068 -- 265 4583 0.1198 0.182 -- 100.0
X Ray Diffraction 5.4068 5.5997 -- 229 4647 0.1162 0.1788 -- 100.0
X Ray Diffraction 5.5997 5.8236 -- 247 4628 0.1091 0.1663 -- 100.0
X Ray Diffraction 5.8236 6.0882 -- 264 4614 0.1164 0.1742 -- 100.0
X Ray Diffraction 6.0882 6.4085 -- 239 4650 0.1192 0.1876 -- 100.0
X Ray Diffraction 6.4085 6.809 -- 232 4674 0.1163 0.1759 -- 100.0
X Ray Diffraction 6.809 7.3332 -- 243 4685 0.1081 0.1622 -- 100.0
X Ray Diffraction 7.3332 8.0682 -- 249 4682 0.1157 0.1733 -- 100.0
X Ray Diffraction 8.0682 9.2288 -- 275 4690 0.1268 0.1779 -- 100.0
X Ray Diffraction 9.2288 11.6017 -- 264 4751 0.1394 0.1842 -- 100.0
X Ray Diffraction 11.6017 48.9133 -- 274 4923 0.2187 0.232 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 146.218
Anisotropic B[1][1] -3.9266
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.9266
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.4395
RMS Deviations
Key Refinement Restraint Deviation
f_dihedral_angle_d 20.411
f_plane_restr 0.009
f_chiral_restr 0.086
f_angle_d 1.627
f_bond_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19127
Nucleic Acid Atoms 33073
Heterogen Atoms 386
Solvent Atoms 892

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