2QHT

Structural Basis of Octanoic Acid Recognition by Lipoate-Protein Ligase B


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729850mM HEPES at pH 7.0, 4.0M lithium chloride, 5%(v/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthew coefficientSolvent content
2.4850.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.609α = 90
b = 63.609β = 90
c = 113.869γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 4MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A0.97925, 0.97942, 0.95000Photon FactoryBL-5A

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
11.52099.60.08111.47.338111
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)
11.51.5599.70.4735.23738

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT1.52038067379299.710.2010.1990.222RANDOM22.579
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]
0.050.05-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.251
r_dihedral_angle_4_deg12.125
r_dihedral_angle_3_deg11.483
r_dihedral_angle_1_deg5.921
r_scangle_it2.986
r_scbond_it1.938
r_angle_refined_deg1.247
r_mcangle_it1.226
r_mcbond_it0.786
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.251
r_dihedral_angle_4_deg12.125
r_dihedral_angle_3_deg11.483
r_dihedral_angle_1_deg5.921
r_scangle_it2.986
r_scbond_it1.938
r_angle_refined_deg1.247
r_mcangle_it1.226
r_mcbond_it0.786
r_nbtor_refined0.314
r_symmetry_vdw_refined0.25
r_nbd_refined0.204
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.157
r_chiral_restr0.078
r_bond_refined_d0.008
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1643
Nucleic Acid Atoms
Solvent Atoms303
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing