5W8A

The structure of a COA-dependent acyl-homoserine lactone synthase, BjaI, with SAM and isopentyl-CoA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52823.0 M sodium chloride, 0.085 M HEPES, pH 7.5, 15% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
4.6173.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.279α = 90
b = 90.279β = 90
c = 98.543γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDRAYONIX MX300HE2014-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.978APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
125099.1538.112.429905
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12

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 DIFFRACTIONMADTHROUGHOUT22529905158899.150.181610.180630.20019RANDOM28.018
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]
0.040.040.04-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.175
r_dihedral_angle_3_deg12.086
r_dihedral_angle_4_deg11.623
r_dihedral_angle_1_deg5.326
r_angle_refined_deg1.223
r_chiral_restr0.078
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.175
r_dihedral_angle_3_deg12.086
r_dihedral_angle_4_deg11.623
r_dihedral_angle_1_deg5.326
r_angle_refined_deg1.223
r_chiral_restr0.078
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1702
Nucleic Acid Atoms
Solvent Atoms255
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing