4MVY | pdb_00004mvy

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-(3-hydroxyphenyl)urea (Chem 1387)

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	68.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.236	α = 90
b = 105.995	β = 90
c = 206.166	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	ADSC QUANTUM 315r		2010-11-21		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00	ALS	8.2.2

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	2.314	50	98.1	0.11	0.11	7.9	6.7		82839		-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	2.314	2.34	93.4		0.791	0.791	2.105	6.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4EG8	2.314	30	82510	4106	97.03	0.1943	0.193	0.19	0.2186	0.21	RANDOM	37.1222

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]
1.71			-0.55		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_4_deg	14.407
r_dihedral_angle_3_deg	13.894
r_dihedral_angle_1_deg	5.5
r_mcangle_it	1.338
r_angle_refined_deg	1.177
r_mcbond_it	0.773
r_mcbond_other	0.773
r_angle_other_deg	0.729
r_chiral_restr	0.067

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.557
r_dihedral_angle_4_deg	14.407
r_dihedral_angle_3_deg	13.894
r_dihedral_angle_1_deg	5.5
r_mcangle_it	1.338
r_angle_refined_deg	1.177
r_mcbond_it	0.773
r_mcbond_other	0.773
r_angle_other_deg	0.729
r_chiral_restr	0.067
r_bond_refined_d	0.007
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	8481
Nucleic Acid Atoms
Solvent Atoms	560
Heterogen Atoms	93

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.