4ZT5

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor (2S)-N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)-2-methylpropane-1,3-diamine (Chem 1655)

X-RAY DIFFRACTION

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
3.89	68.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.794	α = 90
b = 106.021	β = 90
c = 207.659	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	MARMOSAIC 325 mm CCD		2014-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.979	SSRL	BL9-2

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	2.35	39.43	100	0.174	0.046	0.999	17.5	15		80610

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	2.35	2.4	100		1.88	0.496	0.689	1.8	15.1	4543

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	2.35	38.67	76494	4035	99.97	0.2016	0.2001	0.2285	RANDOM	51.265

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]
7.16			-2.74		-4.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_3_deg	13.571
r_dihedral_angle_4_deg	13.19
r_dihedral_angle_1_deg	5.277
r_mcangle_it	2.038
r_mcbond_it	1.247
r_mcbond_other	1.246
r_angle_refined_deg	1.091
r_angle_other_deg	0.884
r_chiral_restr	0.063

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.117
r_dihedral_angle_3_deg	13.571
r_dihedral_angle_4_deg	13.19
r_dihedral_angle_1_deg	5.277
r_mcangle_it	2.038
r_mcbond_it	1.247
r_mcbond_other	1.246
r_angle_refined_deg	1.091
r_angle_other_deg	0.884
r_chiral_restr	0.063
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	8259
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	80

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 R01GM133198.