4V57 | pdb_00004v57

Crystal structure of the bacterial ribosome from Escherichia coli in complex with spectinomycin and neomycin.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AVY	2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AW4	2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AW7	2AVY, 2AW4, 2AW7, 2AWB
experimental model	PDB	2AWB	2AVY, 2AW4, 2AW7, 2AWB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	batch	7.5	277	MPD, PEG 8000, MgCl2, NH4Cl, spermine, spermidine, TRIS, EDTA, pH 7.5, batch, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.41	63.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 208.848	α = 90
b = 379.202	β = 90
c = 739.283	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	93	CCD	ADSC QUANTUM 315		2006-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.111	ALS	12.3.1

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	3.5	182	72.1	0.104	8.6	3.3		521699

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	3.5	3.85	13.9		0.41	1.9	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MOLECULAR REPLACEMENT	2AVY, 2AW4, 2AW7, 2AWB	3.5	70	731327	521145	25274		0.264	0.23	0.306	0.27	74.9

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
bond angles	0.895
bond length	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	18536
Nucleic Acid Atoms	32831
Solvent Atoms	300
Heterogen Atoms	125

Software

Software
Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling
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 R01GM157729.