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Structural Basis of Octanoic Acid Recognition by Lipoate-Protein Ligase B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 50mM HEPES at pH 7.0, 4.0M lithium chloride, 5%(v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.49 50.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.762 α = 90 b = 63.762 β = 90 c = 114.049 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 4 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97925, 0.97942, 0.95000 Photon Factory BL-5A
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 1.9 20 18458
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.9 20 16494 1887 95.67 0.214 0.20561 0.2056 0.24075 0.2404 RANDOM 22.892
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] 0.55 0.55 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_4_deg 15.918 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 5.992 r_scangle_it 2.977 r_scbond_it 1.769 r_angle_refined_deg 1.234 r_mcangle_it 1.127 r_mcbond_it 0.698 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.253 r_dihedral_angle_4_deg 15.918 r_dihedral_angle_3_deg 14.172 r_dihedral_angle_1_deg 5.992 r_scangle_it 2.977 r_scbond_it 1.769 r_angle_refined_deg 1.234 r_mcangle_it 1.127 r_mcbond_it 0.698 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.192 r_xyhbond_nbd_refined 0.146 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 1643 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 9
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SOLVE phasing