6BOH | pdb_00006boh

Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	3 uL of 70SmRNAtRNAfMetRF1antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.
2	VAPOR DIFFUSION, HANGING DROP	7.5	289	3 uL of 70SmRNAtRNAfMetRF1antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.
3	VAPOR DIFFUSION, HANGING DROP	7.5	289	3 uL of 70SmRNAtRNAfMetRF1antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.
4	VAPOR DIFFUSION, HANGING DROP	7.5	289	3 uL of 70SmRNAtRNAfMetRF1antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.
5	VAPOR DIFFUSION, HANGING DROP	7.5	289	3 uL of 70SmRNAtRNAfMetRF1antibiotic complex + 3 uL crystallization buffer (0.1 M Tris-HCl, pH 7.5, 4% v/v PEG20000, 8% v/v MPD, 0.2 M potassium thiocyanate). 4-fold molar excess of E. coli release factor 1 and 1 mM blasticidin S were added during complex formation. Reservoir: 300 uL 0.4-0.6 M sodium chloride.

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.86	α = 90
b = 450.69	β = 90
c = 615.88	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2012-04-14	M	SINGLE WAVELENGTH
2	2	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2012-04-14	M	SINGLE WAVELENGTH
3	3	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2012-03-24	M	SINGLE WAVELENGTH
4	4	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2012-03-24	M	SINGLE WAVELENGTH
5	5	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2012-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D
2	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D
3	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D
4	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D
5	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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
1	3.4	90	100	7.75	38.1		792709

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION		FREE R-VALUE	3.4	50	792518		99.9		0.2428		0.2815

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	95708
Nucleic Acid Atoms	201010
Solvent Atoms
Heterogen Atoms	1498

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.