4YRM | pdb_00004yrm

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 3-methoxypyridine (Chem 443)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LC0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.2 M ammonium sulfate, 23 % to 28 % PEG 3350, 0.1 M sodium citrate pH 4.8 to 5.3, 1 mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.128	α = 90
b = 119.461	β = 91.03
c = 94.552	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU SATURN 944		2013-01-11	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	2.3	35.97	99.2	0.067	0.045	0.999	12.9	3.1		44048

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	2.3	2.38	98.3		0.471	0.326	0.857	2.3	2.8	4279

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	3LC0	2.3	29.87	41781	2255	99.06	0.2155	0.214	0.22	0.2416	0.24	RANDOM	45.038

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]
-0.68		0.59	2.06		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.598
r_dihedral_angle_4_deg	16.517
r_dihedral_angle_3_deg	14.201
r_dihedral_angle_1_deg	5.317
r_angle_refined_deg	1.124
r_mcangle_it	1.115
r_angle_other_deg	0.792
r_mcbond_it	0.657
r_mcbond_other	0.657
r_chiral_restr	0.059

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.598
r_dihedral_angle_4_deg	16.517
r_dihedral_angle_3_deg	14.201
r_dihedral_angle_1_deg	5.317
r_angle_refined_deg	1.124
r_mcangle_it	1.115
r_angle_other_deg	0.792
r_mcbond_it	0.657
r_mcbond_other	0.657
r_chiral_restr	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6387
Nucleic Acid Atoms
Solvent Atoms	276
Heterogen Atoms	89

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

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.