4PY2

Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	289	CSHTa10: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, pH 4.6. 30% PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.01	α = 110.47
b = 99.48	β = 87.24
c = 104	γ = 99.99

Symmetry
Space Group	P 1

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 300 mm CCD	Beryllium Lenses	2014-02-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.15	97.43	98.2	0.066	15.76	3.9	90572	88924		-3	38.461

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.15	2.21	97.3		0.536	2.73

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	FOURIER SYNTHESIS	THROUGHOUT	4LNE	2.15	97.43	93317	88924	4393	98.27	0.1794	0.1777	0.2115	RANDOM	35.976

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]
0.54	0.48	-0.38	-0.95	0.27	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.499
r_dihedral_angle_4_deg	19.823
r_dihedral_angle_3_deg	12.637
r_dihedral_angle_1_deg	5.502
r_mcangle_it	2.203
r_mcbond_it	1.467
r_mcbond_other	1.467
r_angle_refined_deg	1.384
r_angle_other_deg	1.059
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.499
r_dihedral_angle_4_deg	19.823
r_dihedral_angle_3_deg	12.637
r_dihedral_angle_1_deg	5.502
r_mcangle_it	2.203
r_mcbond_it	1.467
r_mcbond_other	1.467
r_angle_refined_deg	1.384
r_angle_other_deg	1.059
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11480
Nucleic Acid Atoms
Solvent Atoms	548
Heterogen Atoms	94

Software

Software
Software Name	Purpose
XSCALE	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.