4V4P

Crystal structure of 70S ribosome with thrS operator and tRNAs.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GIY	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30
experimental model	PDB	1NKW	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30
experimental model	PDB	1AD2	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30
experimental model	PDB	1GD8	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30
experimental model	PDB	1BXE	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30
experimental model	PDB	1BXY	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
5.9	87.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 508.64	α = 90
b = 508.64	β = 90
c = 806.25	γ = 90

Symmetry
Space Group	I 4 2 2

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	MARRESEARCH	Dynamically Bendable Mirror	2004-05-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.97934	SLS	X06SA

Data Collection

Overall
ID #	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
1	5.5	300	97.9	0.096	0.096	13.9	5.4		165570	-3	-3

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	5.5	5.59	94.2		1.83	4.2	7889

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation 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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB entries 1giy (70S ribosome), 1nkw (50S subunit of D. rad. ribosome), 1ad2, 1gd8, 1bxe, 1bxy (T. th. ribosomal proteins L1, L17, L22 and L30	5.5	300	2	165002	160401	7724	94.6	0.314	0.309	0.307	0.356	random	204

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]

RMS Deviations
Key	Refinement Restraint Deviation
c_angle_deg	2.2
c_mcangle_it	1.7
c_mcbond_it	1
c_bond_d	0.016

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27609
Nucleic Acid Atoms	64488
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
HKL-2000	data reduction
CNS	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 R01GM133198.