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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
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 289 CSHTa10: 0.2M ammonium acetate, 0.1M sodium acetate trihydrate, pH 4.6. 30% PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.37 48.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.01 α = 110.47 b = 99.48 β = 87.24 c = 104 γ = 99.99
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2014-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.15 97.43 98.2 0.066 15.76 3.9 90572 88924 -3 38.461
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.21 97.3 0.536 2.73
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4LNE 2.15 97.43 93317 88924 4393 98.27 0.1794 0.1777 0.1859 0.2115 0.2188 RANDOM 35.976
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] 0.54 0.48 -0.38 -0.95 0.27 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.499 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 5.502 r_mcangle_it 2.203 r_mcbond_it 1.467 r_mcbond_other 1.467 r_angle_refined_deg 1.384 r_angle_other_deg 1.059 r_chiral_restr 0.077
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.499 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 12.637 r_dihedral_angle_1_deg 5.502 r_mcangle_it 2.203 r_mcbond_it 1.467 r_mcbond_other 1.467 r_angle_refined_deg 1.384 r_angle_other_deg 1.059 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11480 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 94
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction