3A7A

Crystal structure of E. coli lipoate-protein ligase A in complex with octyl-amp and apoH-protein


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529316.2% 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 coefficientSolvent content
2.7755.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.013α = 90
b = 102.016β = 90
c = 159.934γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402009-03-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1.0000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.965098.10.0719.74.123803
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.11970.48423.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2E5A3.12019375162698.290.232230.228390.27855RANDOM48.457
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]
0.280.44-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.048
r_dihedral_angle_3_deg15.186
r_dihedral_angle_4_deg13.684
r_dihedral_angle_1_deg4.264
r_angle_refined_deg0.636
r_scangle_it0.588
r_mcangle_it0.425
r_scbond_it0.321
r_mcbond_it0.232
r_chiral_restr0.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.048
r_dihedral_angle_3_deg15.186
r_dihedral_angle_4_deg13.684
r_dihedral_angle_1_deg4.264
r_angle_refined_deg0.636
r_scangle_it0.588
r_mcangle_it0.425
r_scbond_it0.321
r_mcbond_it0.232
r_chiral_restr0.043
r_bond_refined_d0.003
r_gen_planes_refined0.002
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 AtomsNumber
Protein Atoms7238
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing