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Crystal structure of methionyl-tRNA synthetase MetRS from Brucella melitensis in complex with inhibitor Chem 1415
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 5 290 BrabA.10201.a.A1.PW37326 at 21.4 mg/ml was mixed 1:1 with PACT(c2): 100 mM PCB buffer, pH=5.0, 25% (w/v) PEG-1500, cryoprotected with 20% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.39 48.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.16 α = 110.46 b = 99.65 β = 88.09 c = 104.3 γ = 99.72
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 225 mm CCD Beryllium Lenses 2014-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.6 50 96 0.075 0.994 10.12 2.4 49660 -3 47.423
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 2.6 2.67 97.5 0.47 2.07 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4LNE 2.6 50 47243 2416 96.13 0.258 0.2565 0.286 0.2612 RANDOM 49.76
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] -2.72 0.86 0.37 1.01 1.78 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 5.313 r_angle_refined_deg 1.183 r_angle_other_deg 1.127 r_mcangle_it 0.683 r_mcbond_it 0.37 r_mcbond_other 0.37 r_chiral_restr 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 13.608 r_dihedral_angle_1_deg 5.313 r_angle_refined_deg 1.183 r_angle_other_deg 1.127 r_mcangle_it 0.683 r_mcbond_it 0.37 r_mcbond_other 0.37 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11165 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 104
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction