4V9D

Structures of the bacterial ribosome in classical and hybrid states of tRNA binding

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I1M	PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1N	PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1O	PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P
experimental model	PDB	3I1P	PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.5	291	PEG8000, MPD, pH 6.5, microbatch, temperature 291K
2	MICROBATCH	6.5	291	PEG8000, MPD, pH 6.5, microbatch, temperature 291K
3	MICROBATCH	6.5	291	PEG8000, MPD, pH 6.5, microbatch, temperature 291K
4	MICROBATCH	6.5	291	PEG8000, MPD, pH 6.5, microbatch, temperature 291K
5	MICROBATCH	6.5	291	PEG8000, MPD, pH 6.5, microbatch, temperature 291K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 211.67	α = 90
b = 438.07	β = 90
c = 613.42	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	CCD	ADSC QUANTUM 315		2010-12-03	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-10-16	M	SINGLE WAVELENGTH
3	1	x-ray	100	CCD	ADSC QUANTUM 315		2010-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1
2	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.1	ALS	12.3.1
3	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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
1,2,3	3	40	83.5	0.194	7.38			938380		-3	51.273

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2,3	3	3.16	43.5		0.816	1.18

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	PDB ENTRIES 3I1M, 3I1N, 3I1O, 3I1P	3	40	1.8	938304	938304	19021		0.203	0.202	0.26	RANDOM	41.6019

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	19973
Nucleic Acid Atoms	34942
Solvent Atoms	203
Heterogen Atoms	72

Software

Software
Software Name	Purpose
XSCALE	data processing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
PHENIX	model building
XDS	data reduction
XDS	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.