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The Structure of the Bifunctional Acetyltransferase/Decarboxylase LnmK from the Leinamycin Biosynthetic Pathway Revealing Novel Activity for a Double Hot Dog Fold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.75 298 Protein solution: 45 mg/mL protein in 10 mM NaCl and 10 mM Tris-HCl, 2.5 mM methylmalonyl-CoA, pH 8.0. Precipitant solution: 12 - 18% glycerol, 1.3 - 1.6 M (NH4)2SO4, 0.1 M Tris-HCl, pH 7.0 - 8.5 (1:1, protein:well), VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.165 α = 90 b = 60.165 β = 90 c = 311.193 γ = 120
Symmetry Space Group P 61 2 2
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 2009-06-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97941, 1.127 APS 21-ID-D
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 2.25 28.06 98.8 0.074 28.7 17.3 17112 16907 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.25 28.06 16907 15889 869 100 0.20245 0.19977 0.1993 0.25381 0.2522 RANDOM 23.1
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.695 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 14.211 r_dihedral_angle_1_deg 6.077 r_scangle_it 2.606 r_scbond_it 1.625 r_angle_refined_deg 1.233 r_mcangle_it 1.098 r_mcbond_it 0.573 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.695 r_dihedral_angle_4_deg 16.91 r_dihedral_angle_3_deg 14.211 r_dihedral_angle_1_deg 6.077 r_scangle_it 2.606 r_scbond_it 1.625 r_angle_refined_deg 1.233 r_mcangle_it 1.098 r_mcbond_it 0.573 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2340 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 39
Software Software Software Name Purpose HKL-2000 data collection SOLVE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling