3DIZ | pdb_00003diz

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine in the Absence of Mg2+

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	53.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54	α = 90
b = 78.803	β = 90
c = 140.631	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	IMAGE PLATE	RIGAKU RAXIS		2008-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.85	20	87	0.105	15.7	3.8	15344	13349

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	2.85	2.95	89.2		0.498	2.7	3.9	1489

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 3DIL	2.85	20	13826	12048	639	87.14	0.19548	0.19548	0.19278	0.2	0.24388	0.25	RANDOM	45.32

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]
-3.43			-4.6		8.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.992
r_angle_refined_deg	1.328
r_scangle_it	0.869
r_scbond_it	0.555
r_mcangle_it	0.406
r_nbtor_refined	0.27
r_mcbond_it	0.207
r_symmetry_hbond_refined	0.187
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.156

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.992
r_angle_refined_deg	1.328
r_scangle_it	0.869
r_scbond_it	0.555
r_mcangle_it	0.406
r_nbtor_refined	0.27
r_mcbond_it	0.207
r_symmetry_hbond_refined	0.187
r_nbd_refined	0.172
r_symmetry_vdw_refined	0.156
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.066
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	10
Heterogen Atoms	23

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	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.