3DIQ | pdb_00003diq

Crystallization of the Thermotoga maritima lysine riboswitch bound to homoarginine

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
2.62	53.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.746	α = 90
b = 78.794	β = 90
c = 140.069	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-E	0.9795	APS	24-ID-E

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	2.7	20	94.9	0.119	13.2	4.7	17041	16172

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)
	2.7	2.8	89		0.56	2.4	4.5	1662

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	REFMAC	THROUGHOUT	pdb entry 3DIL	2.7	20	16081	15261	806	94.9	0.20384	0.20384	0.20182	0.2	0.24134	0.23	RANDOM	24.898

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]
-1.03			-0.63		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.181
r_scangle_it	1.165
r_scbond_it	0.727
r_nbtor_refined	0.266
r_mcangle_it	0.261
r_nbd_refined	0.154
r_symmetry_hbond_refined	0.15
r_symmetry_vdw_refined	0.131
r_xyhbond_nbd_refined	0.13
r_mcbond_it	0.116

RMS Deviations
Key	Refinement Restraint Deviation
r_angle_refined_deg	1.181
r_scangle_it	1.165
r_scbond_it	0.727
r_nbtor_refined	0.266
r_mcangle_it	0.261
r_nbd_refined	0.154
r_symmetry_hbond_refined	0.15
r_symmetry_vdw_refined	0.131
r_xyhbond_nbd_refined	0.13
r_mcbond_it	0.116
r_chiral_restr	0.062
r_metal_ion_refined	0.038
r_bond_refined_d	0.005
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3752
Solvent Atoms	43
Heterogen Atoms	27

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.