8QIC

Structure-based identification of salicylic acid derivatives as malarial threonyl tRNA-synthetase inhibitors

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	5.9	297	10% (w/v) PEG 4000, 18% (v/v) MPD, and 0.1 M sodium citrate pH 5.9

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.78	α = 90
b = 110.5	β = 90
c = 113.97	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 PILATUS 2M-F		2021-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X3A	1	NSLS	X3A

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	2.08	79.34	72.64	0.996	11.2	11.1		47446

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	2.085	2.139			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	2.5	79.33	35571	1932	98.2	0.1969	0.19493	0.23312	RANDOM	36.614

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]
-1.23			0.5		0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.102
r_dihedral_angle_3_deg	14.304
r_long_range_B_refined	8.807
r_long_range_B_other	8.806
r_dihedral_angle_1_deg	6.958
r_scangle_other	6.325
r_scbond_it	4.275
r_scbond_other	4.274
r_mcangle_other	3.696
r_mcangle_it	3.695
r_mcbond_it	2.428
r_mcbond_other	2.416
r_angle_refined_deg	1.311
r_angle_other_deg	0.46
r_chiral_restr	0.061
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6532
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	80

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing