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Crystal structure of E. coli lipoate-protein ligase A in complex with lipoyl-AMP.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E5A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 1.6M Li2SO4, 0.01M MgSO4, 0.05M cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.4 72.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.298 α = 90 b = 102.298 β = 90 c = 221.252 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 ADSC QUANTUM 270 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0000 Photon Factory BL-17A
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 2.05 50 100 0.122 38.1 21.4 44005
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) 2.05 2.12 100 0.472 8.2 20.3 4299
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 MOLECULAR REPLACEMENT THROUGHOUT 2E5A 2.05 20 41478 2204 99.99 0.17701 0.17554 0.20421 0.1874 RANDOM 19.328
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 39.592 r_dihedral_angle_4_deg 18.692 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_1_deg 7.263 r_scangle_it 6.877 r_scbond_it 4.667 r_mcangle_it 2.952 r_mcbond_it 1.847 r_angle_refined_deg 1.119 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.592 r_dihedral_angle_4_deg 18.692 r_dihedral_angle_3_deg 13.297 r_dihedral_angle_1_deg 7.263 r_scangle_it 6.877 r_scbond_it 4.667 r_mcangle_it 2.952 r_mcbond_it 1.847 r_angle_refined_deg 1.119 r_chiral_restr 0.104 r_gen_planes_refined 0.019 r_bond_refined_d 0.01 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 2663 Nucleic Acid Atoms Solvent Atoms 506 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement