8OU8

Crystal structure of E. coli threonyl tRNA synthetase in complex with a TM84 analogue

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QF6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	293	12% (w/v) PEG 4000, 21% (v/v) MPD, and 0.1 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.763131	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.33	α = 90
b = 108.95	β = 90
c = 113.96	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	DECTRIS EIGER2 S 16M		2022-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.05	78.75	99	0.994	9.3	2.2		45827

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.258	48		0.996

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.05	78.75	43429	2397	68.15	0.216	0.18892	0.266	RANDOM	41.717

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]
-0.5			0.18		0.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	19.056
r_dihedral_angle_3_deg	17.127
r_long_range_B_refined	8.625
r_long_range_B_other	8.589
r_dihedral_angle_1_deg	7.775
r_scangle_other	6.424
r_mcangle_it	4.927
r_mcangle_other	4.926
r_scbond_it	4.419
r_scbond_other	4.418
r_mcbond_it	3.511
r_mcbond_other	3.511
r_angle_refined_deg	1.563
r_angle_other_deg	0.522
r_chiral_restr	0.068
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	6560
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	39

Software

Software
Software Name	Purpose
autoPROC	data processing
xia2.multiplex	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement