4ZT2 | pdb_00004zt2

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1575)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystal Properties
Matthews coefficient	Solvent content
3.9	68.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.068	α = 90
b = 106.07	β = 90
c = 207.674	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	RIGAKU SATURN 944		2013-02-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	2.7	35.35	99.7	0.164	0.069	0.995	10.5	6.6		53554

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.78	97.6		0.941	0.419	0.698	1.9	5.8	4475

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	4EG8	2.7	35.35	50766	2720	99.7	0.196	0.1943	0.2	0.2279	0.23	RANDOM	49.103

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]
3.24			-1.41		-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_3_deg	14.154
r_dihedral_angle_4_deg	13.054
r_dihedral_angle_1_deg	5.443
r_mcangle_it	1.719
r_angle_refined_deg	1.116
r_mcbond_it	1.014
r_mcbond_other	1.014
r_angle_other_deg	0.901
r_chiral_restr	0.062

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.961
r_dihedral_angle_3_deg	14.154
r_dihedral_angle_4_deg	13.054
r_dihedral_angle_1_deg	5.443
r_mcangle_it	1.719
r_angle_refined_deg	1.116
r_mcbond_it	1.014
r_mcbond_other	1.014
r_angle_other_deg	0.901
r_chiral_restr	0.062
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8330
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	80

Software

Software
Software Name	Purpose
DENZO	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building

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.