3LN6

Crystal structure of a bifunctional glutathione synthetase from Streptococcus agalactiae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V4G1V4G, 1UC8
experimental modelPDB 1UC81V4G, 1UC8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52981.6M (NH4)2SO4, 100mM Tris-HCl pH 8.5, 12% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1560.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 143.02α = 90
b = 143.02β = 90
c = 211.23γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-02-23MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 210r2008-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7A1.0720EMBL/DESY, HAMBURGBW7A
2SYNCHROTRONESRF BEAMLINE ID14-20.9330ESRFID14-2

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
1,22.92099.60.07723.98.424531-376.731
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.92.9898.10.1321.88.11765

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSIRAS, MRTHROUGHOUT1V4G, 1UC82.952023309117899.90.2530.286RANDOM95.45
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]
-1.03-1.032.07
RMS Deviations
KeyRefinement Restraint Deviation
f_angle_d1.512
f_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5467
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms5

Software

Software
Software NamePurpose
XSCALEdata processing
SOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHASERphasing