4MWB

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[(2,5-dichlorothiophen-3-yl)methyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1509)


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
3.9368.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.138α = 90
b = 106.171β = 90
c = 206.975γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-12-12SINGLE 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 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
12.31338.56799.90.16112.98.28549385493
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)
12.3132.4499.90.0111.1090.77.912305

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4EG82.3133085417427399.860.18140.18050.1982RANDOM37.7066
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]
1.64-0.97-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.116
r_dihedral_angle_4_deg13.961
r_dihedral_angle_3_deg13.404
r_dihedral_angle_1_deg5.398
r_mcangle_it1.599
r_angle_refined_deg1.149
r_mcbond_it0.922
r_mcbond_other0.922
r_angle_other_deg0.732
r_chiral_restr0.066
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.116
r_dihedral_angle_4_deg13.961
r_dihedral_angle_3_deg13.404
r_dihedral_angle_1_deg5.398
r_mcangle_it1.599
r_angle_refined_deg1.149
r_mcbond_it0.922
r_mcbond_other0.922
r_angle_other_deg0.732
r_chiral_restr0.066
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 Atoms8516
Nucleic Acid Atoms
Solvent Atoms428
Heterogen Atoms105

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction