7CBG

Crystal structure of threonyl-tRNA synthetase (ThrRS) from Salmonella enterica in complex with an inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6L2Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.24 M lithium acetate pH 7.5, 18% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.793	α = 90
b = 101.796	β = 90
c = 105.633	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	PIXEL	RIGAKU HyPix-6000HE		2019-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.542

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	2.5	50	99.6	0.039	25.8	5		32934

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	2.5	2.64			0.089	10.9

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	6L2Q	2.5	50	31158	1603	99.1	0.21706	0.21475	0.26126	RANDOM	23.056

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]
1.63			-1.38		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.524
r_dihedral_angle_3_deg	15.002
r_dihedral_angle_4_deg	11.143
r_dihedral_angle_1_deg	5.369
r_long_range_B_refined	1.84
r_long_range_B_other	1.757
r_angle_refined_deg	1.046
r_angle_other_deg	0.871
r_mcangle_it	0.773
r_mcangle_other	0.773
r_mcbond_it	0.407
r_mcbond_other	0.407
r_scangle_other	0.407
r_scbond_it	0.197
r_scbond_other	0.197
r_chiral_restr	0.06
r_bond_refined_d	0.006
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6483
Nucleic Acid Atoms
Solvent Atoms	386
Heterogen Atoms	54

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling
MOLREP	phasing