4XEJ | pdb_00004xej

IRES bound to bacterial Ribosome

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4V83	PDB entry 4V83

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295.5	Initial crystallization screening was performed around conditions previously reported (31, 48) by dispensing 0.2 + 0.2 mL sitting drops with a Phoenix robotic liquid handling system (Art Robbins) on 96-well plates. Once optimal crystallization conditions were determined, crystals were grown by the sitting-drop vapor-diffusion method using drops dispensed by the Phoenix with 1- to 2-mL ribosome complexes mixed with 1-2 mL of reservoir solution [100 mM Tris-OAc, pH 7.0, 200 mM potassium thiocyanate (KSCN), 3.6-5% PEG 20,000, 6-14% 2-methyl-2,4-pentanediol (MPD)] at 22.5C. Crystals emerged after 5-7 d and matured between 2-3 wk. Crystals were then subjected to cryoprotection by gradually replacing the mother liquor with cryoprotection buffer I (100 mM Tris-OAc, pH 7.0, 200 mM KSCN, 5% PEG 20,000, 25% MPD, 14% PEG 200, and 10 mM Mg(OAc)2). The crystals then were flash-frozen by plunging into liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
3.34	63.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.05	α = 90
b = 447.22	β = 90
c = 608.96	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	MARMOSAIC 300 mm CCD		2010-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.033	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	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	3.8	60	99.9	0.2	0.995	8.28	4.8		555726

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.8	4	99.8		1.6	0.998	1.2	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	FREE R-VALUE	PDB entry 4V83	3.8	60	555726	2000	99.9	0.246	0.24	0.284	0.28

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	92320
Nucleic Acid Atoms	194969
Solvent Atoms
Heterogen Atoms	4

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.