6SLL

Diaminobutyrate acetyltransferase EctA from Paenibacillus lautus in complex with its substrate L-2,4-diaminobutyric acid (DAB) and coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6SK1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.2 M sodium fluoride, 20 % (w/v) PEG 3350, 5 mM coenzyme A, 20 mM L-2,4-diaminobutyrate
Crystal Properties
Matthews coefficientSolvent content
2.7455.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.048α = 90
b = 151.048β = 90
c = 46.172γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2017-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9762ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.0575.5399.20.04810.433.59182408
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.051.110.6081.59

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 REPLACEMENTTHROUGHOUT6SK11.275.52116031619199.460.12320.12180.1496RANDOM17.319
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]
0.030.020.03-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_sphericity_free30.51
r_dihedral_angle_4_deg19.694
r_sphericity_bonded11.99
r_dihedral_angle_3_deg11.637
r_rigid_bond_restr7.294
r_dihedral_angle_1_deg7.184
r_angle_refined_deg3.024
r_angle_other_deg1.565
r_chiral_restr0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.953
r_sphericity_free30.51
r_dihedral_angle_4_deg19.694
r_sphericity_bonded11.99
r_dihedral_angle_3_deg11.637
r_rigid_bond_restr7.294
r_dihedral_angle_1_deg7.184
r_angle_refined_deg3.024
r_angle_other_deg1.565
r_chiral_restr0.2
r_bond_refined_d0.039
r_gen_planes_refined0.018
r_gen_planes_other0.008
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2592
Nucleic Acid Atoms
Solvent Atoms543
Heterogen Atoms113

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing