4MVX

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-phenylurea (Chem 1356)


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
3.9268.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.058α = 90
b = 105.956β = 90
c = 206.672γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-05-17SINGLE 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
12.555098.60.1390.1395.44.162918-3
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)
12.552.5999.50.6950.6952.1564.2

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 4EG82.553062638318998.010.20130.1990.2439RANDOM37.2497
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]
3.72-1.62-2.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_3_deg13.948
r_dihedral_angle_4_deg13.727
r_dihedral_angle_1_deg5.426
r_mcangle_it1.976
r_mcbond_it1.088
r_mcbond_other1.088
r_angle_refined_deg1.081
r_angle_other_deg0.706
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.082
r_dihedral_angle_3_deg13.948
r_dihedral_angle_4_deg13.727
r_dihedral_angle_1_deg5.426
r_mcangle_it1.976
r_mcbond_it1.088
r_mcbond_other1.088
r_angle_refined_deg1.081
r_angle_other_deg0.706
r_chiral_restr0.059
r_bond_refined_d0.006
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 Atoms8512
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms106

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction