4ZT7

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-[(4R)-6,8-dichloro-1,2,3,4-tetrahydroquinolin-4-yl]-N'-(5-fluoro-3H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1717)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EG8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	2.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate

Crystal Properties
Matthews coefficient	Solvent content
3.87	68.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.627	α = 90
b = 105.842	β = 90
c = 207.189	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	RIGAKU SATURN 944+		2013-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.4	37.8	99.9	0.136	0.055	0.996	15.3	7		75309

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.45	99.3		0.818	0.446	0.586	1.8	4.3	4363

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	4EG8	2.4	37.8	71386	3795	99.93	0.2088	0.2074	0.2364	RANDOM	37.923

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]
2.91			-0.64		-2.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.104
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_4_deg	13.31
r_dihedral_angle_1_deg	5.397
r_angle_refined_deg	1.115
r_mcangle_it	0.975
r_angle_other_deg	0.913
r_mcbond_it	0.561
r_mcbond_other	0.561
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.104
r_dihedral_angle_3_deg	13.434
r_dihedral_angle_4_deg	13.31
r_dihedral_angle_1_deg	5.397
r_angle_refined_deg	1.115
r_mcangle_it	0.975
r_angle_other_deg	0.913
r_mcbond_it	0.561
r_mcbond_other	0.561
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8322
Nucleic Acid Atoms
Solvent Atoms	507
Heterogen Atoms	58

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

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 R01GM157729.