4PY2

Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor 1-{3-[(3,5-DICHLOROBENZYL)AMINO]PROPYL}-3-THIOPHEN-3-YLUREA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LNE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.6289CSHTa10: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, pH 4.6. 30% PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.3748.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.01α = 110.47
b = 99.48β = 87.24
c = 104γ = 99.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium Lenses2014-02-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.1597.4398.20.06615.763.99057288924-338.461
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2197.30.5362.73

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4LNE2.1597.439331788924439398.270.17940.17770.2115RANDOM35.976
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]
0.540.48-0.38-0.950.270.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.499
r_dihedral_angle_4_deg19.823
r_dihedral_angle_3_deg12.637
r_dihedral_angle_1_deg5.502
r_mcangle_it2.203
r_mcbond_it1.467
r_mcbond_other1.467
r_angle_refined_deg1.384
r_angle_other_deg1.059
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.499
r_dihedral_angle_4_deg19.823
r_dihedral_angle_3_deg12.637
r_dihedral_angle_1_deg5.502
r_mcangle_it2.203
r_mcbond_it1.467
r_mcbond_other1.467
r_angle_refined_deg1.384
r_angle_other_deg1.059
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11480
Nucleic Acid Atoms
Solvent Atoms548
Heterogen Atoms94

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction