3DIO | pdb_00003dio

Crystallization of the Thermotoga maritima lysine riboswitch bound to lysine, IRIDIUM HEXAMINE SOAK

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.7	293	18% PEG4000, 0.1M sodium citrate, 20% isopropanol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.918	α = 90
b = 78.004	β = 90
c = 140.835	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		2008-02-06	M	MAD
2	1
3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.105199	NSLS	X29A
2	SYNCHROTRON	NSLS BEAMLINE X29A	1.105516	NSLS	X29A
3	SYNCHROTRON	NSLS BEAMLINE X29A	1.085799	NSLS	X29A

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	2.4	20	99	0.113	23.9	6.5	24039	23799

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)
	2.4	2.49	97.6		0.539	3.4	6.1	2338

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.4	20	22705	22478	1206	99.02	0.20595	0.20595	0.20397	0.2	0.24319	0.24	RANDOM	27.732

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]
-0.24			-1.38		1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	7.085
r_scangle_it	1.372
r_angle_refined_deg	1.193
r_scbond_it	0.877
r_mcangle_it	0.456
r_mcbond_it	0.287
r_nbtor_refined	0.264
r_nbd_refined	0.154
r_symmetry_vdw_refined	0.127
r_xyhbond_nbd_refined	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	7.085
r_scangle_it	1.372
r_angle_refined_deg	1.193
r_scbond_it	0.877
r_mcangle_it	0.456
r_mcbond_it	0.287
r_nbtor_refined	0.264
r_nbd_refined	0.154
r_symmetry_vdw_refined	0.127
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.12
r_metal_ion_refined	0.097
r_chiral_restr	0.066
r_bond_refined_d	0.006
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms
Nucleic Acid Atoms	3752
Solvent Atoms	259
Heterogen Atoms	156

Software

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