2IL9 | pdb_00002il9

Crystal Structure of Plautia Stali Intestine Virus Intergenic Region Internal Ribosome Entry Site Ribosomal Binding Domain RNA at 3.1 Angstroms

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	303	15% MPD, 150 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 150 mM MgAcetate, 50 mM Na-MES pH 5.6, 5 mM Iridium (III) hexammine, vapor diffusion, sitting drop, temperature 303K
2	VAPOR DIFFUSION, SITTING DROP	5.6	303	15% MPD, 100 mM MgAcetate, 0.5 mM Spermidine; cryoprotected with 20% MPD, 100 mM MgAcetate, 50 mM Na-MES pH 5.6, 5% isopropanol, vapor diffusion, sitting drop, temperature 303K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.57	α = 90
b = 133.57	β = 90
c = 160.425	γ = 120

Symmetry
Space Group	P 63

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 210		2006-04-25	M	MAD
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2006-05-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	1.1053,1.1057,1.1004	ALS	8.2.1
2	ROTATING ANODE	RIGAKU	1.5418

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
1,2	3.1	16.97					26973

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	3.1	16.97	26973	2683	92.4	0.253	0.26	0.294	RANDOM	87.6

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]
-1.15	13.95		-1.15		2.29

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	15.1
c_improper_angle_d	1.39
c_angle_deg	1
c_bond_d	0.005
c_mcbond_it
c_mcangle_it
c_scbond_it
c_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	5665
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
SOLVE	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling

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.