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Crystal Structure of Lipate-Protein Ligase A from Escherichia coli complexed with lipoic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X2G Lipoate protein ligase A from E. coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 ethylene glycol, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3 58.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.2 α = 90 b = 111.6 β = 90 c = 289.6 γ = 90
Symmetry Space Group C 2 2 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 CCD Bruker DIP-6040 mirror 2004-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.92154 SPring-8 BL44XU
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 2.9 200 97.4 0.12 15.6 5 29247 29247 -3
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) 2.9 3 99 0.421 3.8 2939
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 (All) 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 Difference Fourier THROUGHOUT Lipoate protein ligase A from E. coli 2.91 66.67 27666 27666 1533 97.1 0.1907 0.1907 0.1863 0.1838 0.2714 0.2656 RANDOM 39.469
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] 0.59 -0.05 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.855 r_dihedral_angle_3_deg 21.67 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_1_deg 8.038 r_scangle_it 3.692 r_scbond_it 2.238 r_angle_refined_deg 1.976 r_mcangle_it 1.467 r_mcbond_it 0.845 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.855 r_dihedral_angle_3_deg 21.67 r_dihedral_angle_4_deg 19.997 r_dihedral_angle_1_deg 8.038 r_scangle_it 3.692 r_scbond_it 2.238 r_angle_refined_deg 1.976 r_mcangle_it 1.467 r_mcbond_it 0.845 r_nbtor_refined 0.329 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.195 r_xyhbond_nbd_refined 0.169 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 7891 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling