3EGZ

Crystal structure of an in vitro evolved tetracycline aptamer and artificial riboswitch

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	296	0.3 mM RNA, 0.33 mM selenomethionine labeled U1A-RBD double mutant, 0.5 mM chlorotetracycline, 50 mM Tris pH 7.5, 5 mM MgCl2, 0.25 mM spermine; 1uL macromolecular complex:1 uL reservoir; 50 mM HEPES-KOH pH 7.0, 20 mM MGCl2, 12.5-15% PEG 8000; cryo 30% glycerol, 50 mM HEPES-KOH pH 7.0, 20 mM MGCl2, 15% PEG 8000, 0.5 mM spermine, 0.5 mM chlorotetracycline, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.835	α = 90
b = 120.835	β = 90
c = 55.279	γ = 90

Symmetry
Space Group	P 4 21 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	ADSC QUANTUM 315		2008-02-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.9570,0.9797,0.9795	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	2.2	29.31	99.1	0.008	37.6	9.5		21415

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)
	2.2	2.28	99.9		0.532	3.8	9.8	2156

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-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.2	29.31	21171	2156	98.8	0.217	0.212	0.26	RANDOM	50.61

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]
1.12			1.12		-2.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.527
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	15.349
r_dihedral_angle_1_deg	6.36
r_scangle_it	3.276
r_scbond_it	2.081
r_angle_refined_deg	1.987
r_mcangle_it	1.519
r_angle_other_deg	1.27
r_mcbond_it	0.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.527
r_dihedral_angle_4_deg	15.365
r_dihedral_angle_3_deg	15.349
r_dihedral_angle_1_deg	6.36
r_scangle_it	3.276
r_scbond_it	2.081
r_angle_refined_deg	1.987
r_mcangle_it	1.519
r_angle_other_deg	1.27
r_mcbond_it	0.78
r_mcbond_other	0.143
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	727
Nucleic Acid Atoms	1380
Solvent Atoms	146
Heterogen Atoms	45

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.