3V7E

Crystal structure of YbxF bound to the SAM-I riboswitch aptamer

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	294.15	150 M RNA, 210 M YbxF, 10 mM MgCl2, 10 mM SAM, 40 mM KCl, 20 mM HEPES-KOH, 1 mM spermine, 1 mM cobalt hexammine, and 1 mM DTT, 100 mM potassium cacodylate pH 6.0, 200 mM MgCl2 and 25% (v/v) PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 191.762	α = 90
b = 54.305	β = 116.56
c = 106.366	γ = 90

Symmetry
Space Group	C 1 2 1

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 315r		2011-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1	ALS	5.0.2

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	2.8	50		0.098	25.2	4.3	25202	22926		116.2	121.2

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	2.8	2.9	92.7		2.46	4.3	2244

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	M. jannaschii L7Ae protein (PDB ID 1SDS, chain A)	2.8	29.54	22926	2276	93.4	0.218	0.218	0.274	RANDOM	75.6

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]
25.12		15.88	7.19		-32.32

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	18.5
c_scangle_it	6.87
c_mcangle_it	5.58
c_scbond_it	4.99
c_mcbond_it	3.52
c_improper_angle_d	1.73
c_angle_deg	1.4
c_bond_d	0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	962
Nucleic Acid Atoms	5372
Solvent Atoms	15
Heterogen Atoms	202

Software

Software
Software Name	Purpose
ALS	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling