4QRD

Structure of Methionyl-tRNA Synthetase in complex with N-(1H-benzimidazol-2-ylmethyl)-N'-(2,4-dichlorophenyl)-6-(morpholin-4-yl)-1,3,5-triazine-2,4-diamine

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	295	PEG 3350, Tris pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.438	α = 90
b = 76.726	β = 90
c = 118.222	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		2006-07-13	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	1.97	21.25	69.04			28282		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	1.97	2.06	69.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.97	21.25	2	28282	28282	1426	69.04	0.205	0.205	0.2007	0.2829	RANDOM	25.556

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]
0.13			-0.21		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.361
r_dihedral_angle_3_deg	18.404
r_dihedral_angle_4_deg	16.493
r_dihedral_angle_1_deg	6.874
r_scangle_it	2.381
r_angle_refined_deg	1.881
r_scbond_it	1.822
r_mcangle_it	1.224
r_mcbond_it	0.773
r_symmetry_hbond_refined	0.688

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.361
r_dihedral_angle_3_deg	18.404
r_dihedral_angle_4_deg	16.493
r_dihedral_angle_1_deg	6.874
r_scangle_it	2.381
r_angle_refined_deg	1.881
r_scbond_it	1.822
r_mcangle_it	1.224
r_mcbond_it	0.773
r_symmetry_hbond_refined	0.688
r_symmetry_vdw_refined	0.318
r_nbtor_refined	0.312
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.214
r_chiral_restr	0.128
r_metal_ion_refined	0.023
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4220
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	33

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.