3IJL

Structure of dipeptide epimerase from Bacteroides thetaiotaomicron complexed with L-Pro-D-Glu; nonproductive substrate binding.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IJIPDB entry 3IJI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529317% PEG 10000, 0.1M Bis-Tris, 0.1M ammonium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.8456.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.897α = 90
b = 100.074β = 90.34
c = 60.075γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42008-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97915NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.52597.10.08612998512998518.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3IJI1.524.91129985129985654597.10.1920.1920.205RANDOM20.3
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]
1.01-0.5-3.772.75
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.1
c_scangle_it2.51
c_scbond_it1.71
c_mcangle_it1.5
c_angle_deg1.3
c_mcbond_it0.97
c_improper_angle_d0.84
c_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5224
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms36

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling