4QRE

Structure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	295	PEG3350, Tris pH 7.9, ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.932	α = 90
b = 75.672	β = 90
c = 119.16	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	IMAGE PLATE	MAR scanner 345 mm plate		2007-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	21.5	94.5			61657	58516	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.78	94.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.7	21.45	61660	3141	94.49	0.2042	0.2024	0.2395	RANDOM	24.284

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]
-0.04			0.14		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.033
r_dihedral_angle_4_deg	14.328
r_dihedral_angle_3_deg	12.938
r_dihedral_angle_1_deg	6.8
r_scangle_it	2.053
r_angle_refined_deg	1.791
r_scbond_it	1.425
r_mcangle_it	0.87
r_mcbond_it	0.54
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.033
r_dihedral_angle_4_deg	14.328
r_dihedral_angle_3_deg	12.938
r_dihedral_angle_1_deg	6.8
r_scangle_it	2.053
r_angle_refined_deg	1.791
r_scbond_it	1.425
r_mcangle_it	0.87
r_mcbond_it	0.54
r_nbtor_refined	0.315
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.161
r_symmetry_hbond_refined	0.141
r_xyhbond_nbd_refined	0.115
r_chiral_restr	0.093
r_metal_ion_refined	0.048
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4220
Nucleic Acid Atoms
Solvent Atoms	615
Heterogen Atoms	71

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALEPACK	data scaling
PHASER	phasing
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 R01GM133198.