4YRS

Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with N-(quinolin-3-yl)propanamide (Chem 1698)


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
2.5952.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.455α = 90
b = 119.677β = 94.17
c = 66.75γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.95SSRLBL12-2

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
12.7537.8196.20.0540.030.999174.113023
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)
12.752.997.60.7290.4020.73224.21938

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 REPLACEMENTTHROUGHOUT3LC02.7537.811236165795.920.18340.18070.2371RANDOM78.757
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]
4.24-2.29-0.53-3.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.595
r_dihedral_angle_4_deg18.72
r_dihedral_angle_3_deg14.379
r_dihedral_angle_1_deg5.527
r_mcangle_it2.497
r_mcbond_it1.477
r_mcbond_other1.477
r_angle_refined_deg1.112
r_angle_other_deg0.716
r_chiral_restr0.057
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.595
r_dihedral_angle_4_deg18.72
r_dihedral_angle_3_deg14.379
r_dihedral_angle_1_deg5.527
r_mcangle_it2.497
r_mcbond_it1.477
r_mcbond_other1.477
r_angle_refined_deg1.112
r_angle_other_deg0.716
r_chiral_restr0.057
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3234
Nucleic Acid Atoms
Solvent Atoms30
Heterogen Atoms26

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing