5ICL

Crystal structure of Enterococcus faecalis lipoate-protein ligase A (lplA-2) in complex with lipoyl-AMP


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.252891.5 UL PROTEIN + 1.5 UL BUFFER (31% PEG3350, 0.1 M SODIUM CACODYLATE, 0.2 M SODIUM CHLORIDE, PH 5.25)
Crystal Properties
Matthews coefficientSolvent content
2.1342.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.942α = 90
b = 69.35β = 92.15
c = 97.685γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-ID-D

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
11.85099.70.05811.54.262746
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)
11.81.8399.70.3544.2

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 REPLACEMENTTHROUGHOUT5IBY1.84859481318099.330.19940.19750.2351RANDOM28.509
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]
-0.360.441.27-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.507
r_dihedral_angle_4_deg13.705
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.99
r_mcangle_it2.567
r_mcbond_it1.905
r_mcbond_other1.905
r_angle_refined_deg1.165
r_angle_other_deg0.721
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.507
r_dihedral_angle_4_deg13.705
r_dihedral_angle_3_deg11.744
r_dihedral_angle_1_deg5.99
r_mcangle_it2.567
r_mcbond_it1.905
r_mcbond_other1.905
r_angle_refined_deg1.165
r_angle_other_deg0.721
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5183
Nucleic Acid Atoms
Solvent Atoms408
Heterogen Atoms68

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
DENZOdata reduction