3K1G

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Ser-L-Tyr


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3JVA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52901.4M Sodium Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal Properties
Matthews coefficientSolvent content
2.7154.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 163.663α = 90
b = 163.663β = 90
c = 318.051γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42009-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X4A0.97915NSLSX4A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
122599.921431321431325.7

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3JVA224.732143132143131075299.90.2470.2450.2450.282RANDOM41.1
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]
1.13.211.1-2.2
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.6
c_scangle_it2.83
c_scbond_it1.94
c_mcangle_it1.85
c_mcbond_it1.23
c_angle_deg1.2
c_improper_angle_d0.71
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms21170
Nucleic Acid Atoms
Solvent Atoms485
Heterogen Atoms208

Software

Software
Software NamePurpose
ADSCdata collection
BALBESphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling