4YRF

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 5-bromopyridin-2(1H)-one (Chem 148)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LC0 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.2 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 coefficientSolvent content
2.4650.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.433α = 90
b = 118.814β = 92.39
c = 65.975γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442013-02-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.228.9598.60.0440.0310.999182.724799
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)RedundancyNumber Unique Reflections (All)
12.22.2796.30.3740.2820.8642.22.22066

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3LC02.228.9523499129398.550.21380.21130.2611RANDOM56.17
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]
-4.540.155.98-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_3_deg13.983
r_dihedral_angle_4_deg13.27
r_dihedral_angle_1_deg5.5
r_angle_refined_deg1.058
r_mcangle_it0.78
r_angle_other_deg0.719
r_mcbond_it0.425
r_mcbond_other0.422
r_chiral_restr0.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.413
r_dihedral_angle_3_deg13.983
r_dihedral_angle_4_deg13.27
r_dihedral_angle_1_deg5.5
r_angle_refined_deg1.058
r_mcangle_it0.78
r_angle_other_deg0.719
r_mcbond_it0.425
r_mcbond_other0.422
r_chiral_restr0.054
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3127
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing