3DIX

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, K+ anomalous data

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DIL	pdb entry 3DIL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	18% PEG 4000, 0.1M Sodium Citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.108	α = 90
b = 78.902	β = 90
c = 140.167	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	ADSC QUANTUM 4		2008-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	1.84	APS	24-ID-C

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	2.9	20	97.5	0.118	12.4	4.3	13870	13523

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	2.9	3	97.3		0.331	2.5	3.6	1325

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 3DIL	2.9	20	13142	12821	670	97.56	0.17278	0.17278	0.1711	0.20525	RANDOM	34.281

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]
0.09			-1.36		1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.531
r_angle_refined_deg	1.259
r_scangle_it	0.997
r_scbond_it	0.614
r_nbtor_refined	0.266
r_mcangle_it	0.245
r_mcbond_it	0.161
r_symmetry_vdw_refined	0.16
r_nbd_refined	0.159
r_symmetry_hbond_refined	0.151

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	10.531
r_angle_refined_deg	1.259
r_scangle_it	0.997
r_scbond_it	0.614
r_nbtor_refined	0.266
r_mcangle_it	0.245
r_mcbond_it	0.161
r_symmetry_vdw_refined	0.16
r_nbd_refined	0.159
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.109
r_chiral_restr	0.055
r_metal_ion_refined	0.031
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3752
Solvent Atoms	18
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	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.