4MW2

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-(3-{[5-chloro-2-hydroxy-3-(prop-2-en-1-yl)benzyl]amino}propyl)-3-thiophen-3-ylurea (Chem 1472)


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
3.9168.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.712α = 90
b = 106.08β = 90
c = 206.275γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-06-19SINGLE 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
12.35096.30.1060.1065.86.482816-3
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)
12.32.3488.70.7280.72825.9

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4EG82.33082518412595.940.20430.20260.2378RANDOM47.5478
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]
7.4-4.31-3.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_3_deg13.902
r_dihedral_angle_4_deg12.864
r_dihedral_angle_1_deg5.445
r_mcangle_it1.552
r_angle_refined_deg1.165
r_mcbond_it0.916
r_mcbond_other0.916
r_angle_other_deg0.734
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_3_deg13.902
r_dihedral_angle_4_deg12.864
r_dihedral_angle_1_deg5.445
r_mcangle_it1.552
r_angle_refined_deg1.165
r_mcbond_it0.916
r_mcbond_other0.916
r_angle_other_deg0.734
r_chiral_restr0.065
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 Atoms8416
Nucleic Acid Atoms
Solvent Atoms269
Heterogen Atoms146

Software

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