4MVX

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea (Chem 1356)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EG8	PDB ENTRY 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, pH 6.0-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.058	α = 90
b = 105.956	β = 90
c = 206.672	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		2011-05-17		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.98	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.55	50	98.6	0.139	0.139	5.4	4.1		62918		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	99.5		0.695	0.695	2.156	4.2

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	RIGID BODY REFINEMENT OF ISOMORPHOUS STRUCTURE	THROUGHOUT	PDB ENTRY 4EG8	2.55	30	62638	3189	98.01	0.2013	0.199	0.2439	RANDOM	37.2497

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]
3.72			-1.62		-2.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.082
r_dihedral_angle_3_deg	13.948
r_dihedral_angle_4_deg	13.727
r_dihedral_angle_1_deg	5.426
r_mcangle_it	1.976
r_mcbond_it	1.088
r_mcbond_other	1.088
r_angle_refined_deg	1.081
r_angle_other_deg	0.706
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.082
r_dihedral_angle_3_deg	13.948
r_dihedral_angle_4_deg	13.727
r_dihedral_angle_1_deg	5.426
r_mcangle_it	1.976
r_mcbond_it	1.088
r_mcbond_other	1.088
r_angle_refined_deg	1.081
r_angle_other_deg	0.706
r_chiral_restr	0.059
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8512
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	106

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

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.