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Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein
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 8.5 293 16.2% PEG 3350, 0.045M MgSO4, 0.045M NaCl, 1mM NiCl2, 2% Polyethylene glycol monomethyl ether 2000, 0.01M Tris-Cl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.013 α = 90 b = 102.016 β = 90 c = 159.934 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 CCD Bruker DIP-6040 2009-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 1.0000 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 2.96 50 98.1 0.07 19.7 4.1 23803
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) 1 3 3.11 97 0.484 2 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2E5A 3.1 20 19375 1626 98.29 0.23223 0.22839 0.21 0.27855 0.2766 RANDOM 48.457
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] 0.28 0.44 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_4_deg 13.684 r_dihedral_angle_1_deg 4.264 r_angle_refined_deg 0.636 r_scangle_it 0.588 r_mcangle_it 0.425 r_scbond_it 0.321 r_mcbond_it 0.232 r_chiral_restr 0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.048 r_dihedral_angle_3_deg 15.186 r_dihedral_angle_4_deg 13.684 r_dihedral_angle_1_deg 4.264 r_angle_refined_deg 0.636 r_scangle_it 0.588 r_mcangle_it 0.425 r_scbond_it 0.321 r_mcbond_it 0.232 r_chiral_restr 0.043 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 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 7238 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing