4MW5

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor 1-{3-[(3-chloro-5-methoxybenzyl)amino]propyl}-3-phenylurea (Chem 1415)


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
3.8968.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.449α = 90
b = 105.728β = 90
c = 206.592γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-11-21SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.00ALS8.2.2

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
12.347501000.1320.1326.97.480839-3
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)
12.3472.3999.90.8760.8762.0777.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4EG82.3473080530403999.580.19010.18860.2174RANDOM36.8481
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]
3.45-1.55-1.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.449
r_dihedral_angle_4_deg14.772
r_dihedral_angle_3_deg13.743
r_dihedral_angle_1_deg5.629
r_mcangle_it1.753
r_angle_refined_deg1.195
r_mcbond_it0.998
r_mcbond_other0.998
r_angle_other_deg0.728
r_chiral_restr0.068
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.449
r_dihedral_angle_4_deg14.772
r_dihedral_angle_3_deg13.743
r_dihedral_angle_1_deg5.629
r_mcangle_it1.753
r_angle_refined_deg1.195
r_mcbond_it0.998
r_mcbond_other0.998
r_angle_other_deg0.728
r_chiral_restr0.068
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8450
Nucleic Acid Atoms
Solvent Atoms544
Heterogen Atoms102

Software

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