6SL8

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2850.2 M sodium sulphate, 20 % (w/v) PEG 3350, 0.1 M Bis-Tris propane pH 8.5, 20 mM L-2,4-diaminobutyrate
Crystal Properties
Matthews coefficientSolvent content
3.1260.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.979α = 90
b = 57.979β = 90
c = 134.461γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 4M2017-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.9677ESRFMASSIF-1

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
11.5153.2499.90.05316.648.836817
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)
11.511.699.91.4531.328.8

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 REPLACEMENTTHROUGHOUT6SLL1.5353.2433578173699.650.17920.17750.214RANDOM31.658
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.72
r_dihedral_angle_4_deg19.137
r_dihedral_angle_3_deg12.694
r_dihedral_angle_1_deg6.302
r_angle_refined_deg2.345
r_angle_other_deg1.163
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.72
r_dihedral_angle_4_deg19.137
r_dihedral_angle_3_deg12.694
r_dihedral_angle_1_deg6.302
r_angle_refined_deg2.345
r_angle_other_deg1.163
r_chiral_restr0.145
r_bond_refined_d0.024
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1267
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms25

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing