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Structure of Methionyl-tRNA Synthetase in complex with 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 295 PEG3350, Tris pH 7.9, ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.932 α = 90 b = 75.672 β = 90 c = 119.16 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2007-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.7 21.5 94.5 61657 58516 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.78 94.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 MOLECULAR REPLACEMENT THROUGHOUT 1.7 21.45 61660 3141 94.49 0.2042 0.2024 0.1972 0.2395 0.2317 RANDOM 24.284
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] -0.04 0.14 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 14.328 r_dihedral_angle_3_deg 12.938 r_dihedral_angle_1_deg 6.8 r_scangle_it 2.053 r_angle_refined_deg 1.791 r_scbond_it 1.425 r_mcangle_it 0.87 r_mcbond_it 0.54 r_nbtor_refined 0.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.033 r_dihedral_angle_4_deg 14.328 r_dihedral_angle_3_deg 12.938 r_dihedral_angle_1_deg 6.8 r_scangle_it 2.053 r_angle_refined_deg 1.791 r_scbond_it 1.425 r_mcangle_it 0.87 r_mcbond_it 0.54 r_nbtor_refined 0.315 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.093 r_metal_ion_refined 0.048 r_bond_refined_d 0.011 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4220 Nucleic Acid Atoms Solvent Atoms 615 Heterogen Atoms 71
Software Software Software Name Purpose MOSFLM data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction