4MW6

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[2-(benzyloxy)-5-chloro-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1476)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4EG8PDB ENTRY 4EG8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2982.0-2.3 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M sodium cacodylate, pH 6.0-6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.968.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.277α = 90
b = 106.135β = 90
c = 207.057γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-05-20SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL12-20.98SSRLBL12-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.555099.60.1430.14356.462498-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.552.5997.50.7320.7321.9525.9

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 DIFFRACTIONRIGID BODY REFINEMENT OF ISOMORPHOUS STRUCTURETHROUGHOUTPDB ENTRY 4EG82.5583062214316998.870.20280.20070.2412RANDOM45.4211
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]
6.13-2.67-3.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_3_deg14.218
r_dihedral_angle_4_deg14.2
r_dihedral_angle_1_deg5.362
r_mcangle_it2.184
r_mcbond_it1.25
r_mcbond_other1.25
r_angle_refined_deg1.16
r_angle_other_deg0.725
r_chiral_restr0.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.536
r_dihedral_angle_3_deg14.218
r_dihedral_angle_4_deg14.2
r_dihedral_angle_1_deg5.362
r_mcangle_it2.184
r_mcbond_it1.25
r_mcbond_other1.25
r_angle_refined_deg1.16
r_angle_other_deg0.725
r_chiral_restr0.063
r_bond_refined_d0.008
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 Atoms8484
Nucleic Acid Atoms
Solvent Atoms338
Heterogen Atoms117

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction