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