6WNS

The structure of a CoA-dependent acyl-homoserine lactone synthase, MesI


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2820.1 M sodium cacodylate, pH 6.5, 40% v/v MPD, 5% w/v PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.6553.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.673α = 90
b = 65.673β = 90
c = 113.539γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARMOSAIC 300 mm CCD2017-04-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97857APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.9356.899.8137.92019634
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.931.930.842

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEPDB entry 5W8E1.9356.81963398699.7460.2160.21460.234866.755
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]
0.7650.765-1.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.121
r_dihedral_angle_3_deg17.746
r_dihedral_angle_4_deg17.234
r_lrange_it11.058
r_lrange_other11.042
r_dihedral_angle_1_deg7.637
r_scangle_it5.211
r_scangle_other5.209
r_mcangle_it4.033
r_mcangle_other4.031
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.121
r_dihedral_angle_3_deg17.746
r_dihedral_angle_4_deg17.234
r_lrange_it11.058
r_lrange_other11.042
r_dihedral_angle_1_deg7.637
r_scangle_it5.211
r_scangle_other5.209
r_mcangle_it4.033
r_mcangle_other4.031
r_scbond_it3.492
r_scbond_other3.49
r_mcbond_it2.922
r_mcbond_other2.921
r_angle_refined_deg1.989
r_angle_other_deg1.481
r_xyhbond_nbd_refined0.29
r_symmetry_xyhbond_nbd_other0.274
r_nbd_refined0.268
r_nbd_other0.26
r_symmetry_nbd_other0.208
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.18
r_chiral_restr0.098
r_symmetry_nbd_refined0.095
r_symmetry_nbtor_other0.085
r_bond_refined_d0.018
r_gen_planes_refined0.014
r_xyhbond_nbd_other0.013
r_bond_other_d0.006
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1558
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
XDSdata scaling
PHASERphasing