4EX5

Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to lysine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	ButhA.00612.a.A1 PS01208 at 18.9 mg/mL against Morpheus H5, 10% PEG 20,000, 20% PEG 550 MME, 0.1 M MOPS/Hepes, 20 mM glutamate, 20 mM alanine, 20 mM glycine, 20 mM serine, 20 mM lysine, crystal tracking ID 232983h5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.73	66.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.22	α = 90
b = 118.54	β = 113.23
c = 94.54	γ = 90

Symmetry
Space Group	P 1 21 1

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	RIGAKU SATURN 944+		2012-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	50	98.1	0.08	10.87	2.8	68404	67117		-3	39.185

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	2.4	2.46	96.1		0.468	2.27

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1bbu	2.4	50	67095	3401	98.27	0.1909	0.1892	0.2228	RANDOM	32.9777

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]
0.31		0.86	-1.21		1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.826
r_dihedral_angle_4_deg	17.592
r_dihedral_angle_3_deg	14.361
r_dihedral_angle_1_deg	6.003
r_angle_refined_deg	1.444
r_angle_other_deg	1.103
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.826
r_dihedral_angle_4_deg	17.592
r_dihedral_angle_3_deg	14.361
r_dihedral_angle_1_deg	6.003
r_angle_refined_deg	1.444
r_angle_other_deg	1.103
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7588
Nucleic Acid Atoms
Solvent Atoms	461
Heterogen Atoms	20

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

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.