6SWX

Leishmania major methionyl-tRNA synthetase in complex with an allosteric inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	23-28% PEG 3350, 0.2 M K Formate pH 7.0-7.5

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.178	α = 90
b = 100.791	β = 90
c = 132.056	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 6M		2017-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	28.55	99.8	0.037	1	24	6.5		53240			35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	98		0.711	0.87	2.4	6.6

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	3KFL	1.95	28.55	50467	2702	99.81	0.1874	0.186	0.214	RANDOM	45.156

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]
3.19			-0.38		-2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.962
r_dihedral_angle_4_deg	16.042
r_dihedral_angle_3_deg	14.745
r_dihedral_angle_1_deg	7.232
r_mcangle_it	5.721
r_mcbond_it	4.521
r_mcbond_other	4.52
r_angle_other_deg	2.312
r_angle_refined_deg	1.65
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.962
r_dihedral_angle_4_deg	16.042
r_dihedral_angle_3_deg	14.745
r_dihedral_angle_1_deg	7.232
r_mcangle_it	5.721
r_mcbond_it	4.521
r_mcbond_other	4.52
r_angle_other_deg	2.312
r_angle_refined_deg	1.65
r_chiral_restr	0.081
r_bond_other_d	0.035
r_gen_planes_other	0.017
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4232
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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.