5IJ6

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-1) in complex with lipoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5IBY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52890.5 UL PROTEIN + 0.5 UL BUFFER (30% PEG 4K, 0.2 M LITHIUM SULFATE, 0.1 M Tris HCl, PH 8.5)
Crystal Properties
Matthews coefficientSolvent content
2.4549.87

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.011α = 90
b = 70.912β = 90
c = 106.466γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002015-10-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
1239.441000.1450.1540.0520.9949.18.627879
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.051000.5930.6290.2080.9188.92145

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 REPLACEMENTTHROUGHOUT5IBY239.4726261141499.330.17930.17780.207RANDOM33.667
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]
-0.921.36-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.52
r_dihedral_angle_4_deg12.697
r_dihedral_angle_3_deg12.627
r_dihedral_angle_1_deg6.028
r_angle_refined_deg1.174
r_angle_other_deg0.707
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.52
r_dihedral_angle_4_deg12.697
r_dihedral_angle_3_deg12.627
r_dihedral_angle_1_deg6.028
r_angle_refined_deg1.174
r_angle_other_deg0.707
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2602
Nucleic Acid Atoms
Solvent Atoms178
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction