5WIT

Crystal structure of the Thermus thermophilus 70S ribosome in complex with pikromycin and bound to mRNA and A-, P- and E-site tRNAs at 2.6A resolution


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.6
Temperature 292.0
Details 0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.5% PEG-20K, 7-12% MPD, 0.5 mM BME

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 209.34 α = 90
b = 447.21 β = 90
c = 620.61 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-F S/N 60-0112-F 2016-03-26
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97950 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
2.6 152.82 98.3 0.139 -- -- 3.346 -- 1729501 -- -3.0 49.2
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)
2.6 2.67 96.4 1.221 -- 0.97 3.191 --

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 2.6 152.82 -- 1.34 -- 1729334 86836 98.27 -- 0.2407 0.2385 0.2833 --
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 2.6 2.6295 -- 2718 51896 0.3621 0.3971 0.0 94.0
X Ray Diffraction 2.6295 2.6605 -- 2974 54514 0.3486 0.383 0.0 99.0
X Ray Diffraction 2.6605 2.6929 -- 2861 54822 0.3406 0.3792 0.0 99.0
X Ray Diffraction 2.6929 2.727 -- 2888 54754 0.3319 0.3755 0.0 99.0
X Ray Diffraction 2.727 2.7629 -- 2836 54742 0.3288 0.3718 0.0 99.0
X Ray Diffraction 2.7629 2.8008 -- 2926 54639 0.3311 0.3795 0.0 99.0
X Ray Diffraction 2.8008 2.8408 -- 2928 54534 0.3442 0.3868 0.0 98.0
X Ray Diffraction 2.8408 2.8832 -- 2896 54304 0.3484 0.3943 0.0 98.0
X Ray Diffraction 2.8832 2.9282 -- 2875 53554 0.3314 0.3785 0.0 97.0
X Ray Diffraction 2.9282 2.9763 -- 2889 55070 0.3129 0.3604 0.0 99.0
X Ray Diffraction 2.9763 3.0276 -- 2914 55124 0.2859 0.3412 0.0 99.0
X Ray Diffraction 3.0276 3.0826 -- 2901 55173 0.2822 0.3328 0.0 99.0
X Ray Diffraction 3.0826 3.1419 -- 2886 55041 0.2762 0.3285 0.0 99.0
X Ray Diffraction 3.1419 3.2061 -- 2872 55045 0.2703 0.3163 0.0 99.0
X Ray Diffraction 3.2061 3.2758 -- 2870 55143 0.2688 0.313 0.0 99.0
X Ray Diffraction 3.2758 3.352 -- 2850 54798 0.2609 0.3137 0.0 99.0
X Ray Diffraction 3.352 3.4358 -- 2909 55050 0.255 0.3105 0.0 99.0
X Ray Diffraction 3.4358 3.5287 -- 2920 54746 0.2501 0.299 0.0 99.0
X Ray Diffraction 3.5287 3.6326 -- 2791 53479 0.2419 0.2864 0.0 96.0
X Ray Diffraction 3.6326 3.7498 -- 2928 55134 0.2372 0.2835 0.0 99.0
X Ray Diffraction 3.7498 3.8839 -- 2880 55184 0.2333 0.2751 0.0 99.0
X Ray Diffraction 3.8839 4.0394 -- 2893 55065 0.2264 0.2764 0.0 99.0
X Ray Diffraction 4.0394 4.2232 -- 2950 55062 0.2216 0.2626 0.0 99.0
X Ray Diffraction 4.2232 4.4459 -- 2902 55041 0.2146 0.2549 0.0 99.0
X Ray Diffraction 4.4459 4.7245 -- 2864 53788 0.2059 0.2497 0.0 96.0
X Ray Diffraction 4.7245 5.0893 -- 2894 54825 0.1952 0.2354 0.0 98.0
X Ray Diffraction 5.0893 5.6014 -- 2950 55260 0.1862 0.2297 0.0 99.0
X Ray Diffraction 5.6014 6.412 -- 2968 55537 0.1836 0.2345 0.0 99.0
X Ray Diffraction 6.412 8.0784 -- 2923 55135 0.174 0.2215 0.0 98.0
X Ray Diffraction 8.0784 153.085 -- 2980 56039 0.178 0.2095 0.0 97.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 52.6941
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.04
f_dihedral_angle_d 14.53
f_angle_d 0.838
f_bond_d 0.004
f_plane_restr 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 91002
Nucleic Acid Atoms 202011
Heterogen Atoms 5464
Solvent Atoms 427

Software

Software
Software Name Purpose
XDS data reduction
XSCALE data scaling
PHASER phasing
PHENIX refinement version: 1.8.2
Coot model building version: 0.8.2
PDB_EXTRACT data extraction version: 3.22