4YRO

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with 5-bromo-6-methylpyridin-2-amine (Chem 491)


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
2.4750.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.63α = 90
b = 118.264β = 92.52
c = 66.109γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442012-12-04MSINGLE 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
12.533.8598.40.0630.050.99714.42.316909
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)
12.52.699.20.4350.3450.8042.22.31931

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 REPLACEMENTTHROUGHOUT3LC02.5301603687198.280.18830.18610.2309RANDOM61.119
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]
-1.130.113.75-2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.799
r_dihedral_angle_4_deg18.836
r_dihedral_angle_3_deg14.954
r_dihedral_angle_1_deg5.82
r_mcangle_it1.401
r_angle_refined_deg1.18
r_mcbond_it0.827
r_mcbond_other0.827
r_angle_other_deg0.733
r_chiral_restr0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.799
r_dihedral_angle_4_deg18.836
r_dihedral_angle_3_deg14.954
r_dihedral_angle_1_deg5.82
r_mcangle_it1.401
r_angle_refined_deg1.18
r_mcbond_it0.827
r_mcbond_other0.827
r_angle_other_deg0.733
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3251
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms51

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing