4MVW

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3,5-dichlorobenzyl)amino]propyl}-3-thiophen-3-ylurea (Chem 1433)


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
3.9268.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.066α = 90
b = 105.858β = 90
c = 206.974γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442010-10-23SINGLE 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)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
12.9015099.90.2020.2024.76.743617-3
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)
12.90131000.8310.8312.0586.4

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 4EG82.9013043364218599.280.19550.19270.2487RANDOM43.0186
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]
2.73-0.89-1.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.536
r_dihedral_angle_4_deg15.516
r_dihedral_angle_3_deg14.478
r_dihedral_angle_1_deg5.289
r_mcangle_it1.325
r_angle_refined_deg1.059
r_mcbond_it0.736
r_mcbond_other0.736
r_angle_other_deg0.702
r_chiral_restr0.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.536
r_dihedral_angle_4_deg15.516
r_dihedral_angle_3_deg14.478
r_dihedral_angle_1_deg5.289
r_mcangle_it1.325
r_angle_refined_deg1.059
r_mcbond_it0.736
r_mcbond_other0.736
r_angle_other_deg0.702
r_chiral_restr0.058
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 Atoms8487
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms98

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction