7T1Q

Crystal Structure of the Succinyl-diaminopimelate Desuccinylase (DapE) from Acinetobacter baumannii in complex with Succinic Acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5292Protein: 10.6 mg/ml, 0.15M Sodium chloride, 0.01M Tris pH 8.3, 2mM N6-Me-L,L-SDAP; Screen: Classics II (D5), 0.1M Sodium acetate pH 4.5, 25% (w/v) PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.9458.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.323α = 90
b = 103.46β = 90
c = 145.157γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9Mmirrors2021-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D0.97848APS21-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.25301000.1450.1450.1510.0430.99720.212.250400-345.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.291000.6070.7561.712.5

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 REPLACEMENTTHROUGHOUT5uej2.2529.7147108245899.90.190.18780.2331RANDOM53.815
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]
4.810.49-5.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.932
r_dihedral_angle_4_deg11.05
r_dihedral_angle_3_deg7.645
r_dihedral_angle_1_deg2.112
r_angle_refined_deg1.352
r_angle_other_deg0.361
r_chiral_restr0.058
r_gen_planes_refined0.052
r_gen_planes_other0.047
r_bond_refined_d0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.932
r_dihedral_angle_4_deg11.05
r_dihedral_angle_3_deg7.645
r_dihedral_angle_1_deg2.112
r_angle_refined_deg1.352
r_angle_other_deg0.361
r_chiral_restr0.058
r_gen_planes_refined0.052
r_gen_planes_other0.047
r_bond_refined_d0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5772
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing