5AGR

Crystal structure of the LeuRS editing domain of Mycobacterium tuberculosis in complex with the adduct (S)-3-(Aminomethyl)-7-ethoxybenzo[c][1,2]oxaborol-1(3H)-ol-AMP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AJG	PDB ENTRY 2AJG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5.5		0.1 M BIS-TRIS PH 5.5, 17% W/V PEG 10000, 0.2 M AMMONIUM ACETATE

Crystal Properties
Matthews coefficient	Solvent content
2.1	42.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.33	α = 90
b = 61.85	β = 90
c = 77.08	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	MARMOSAIC 225 mm CCD		2010-07-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	1.3	35.5	96.8	0.05	14.4	4.3		48494		2

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	1.3	1.33	98.9		0.98	1.9	4

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 2AJG	1.3	38.54	48494	2668	96.76	0.17059	0.16915	0.19657	RANDOM	18.222

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]
0.54			0.16		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.86
r_dihedral_angle_3_deg	13.351
r_dihedral_angle_4_deg	10.337
r_dihedral_angle_1_deg	5.716
r_scangle_it	3.203
r_scbond_it	2.104
r_angle_refined_deg	1.511
r_mcangle_it	1.475
r_rigid_bond_restr	0.94
r_mcbond_it	0.845
r_chiral_restr	0.147
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1414
Nucleic Acid Atoms
Solvent Atoms	267
Heterogen Atoms	57

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing