Cyclodipeptide Synthase from Fusarium oxysporum (Se-Met)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293Custom screen based on BCS screen well-A6 0.1 M MES pH 6.5 22.5 % PEG smear Medium 7.5 mg/ml Protein 1:1 P:R Streak seed with native crystals using whisker from pet dog (dogs name = Louie)
Crystal Properties
Matthews coefficientSolvent content
2.3948.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.59α = 90
b = 113.062β = 103.46
c = 60.117γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.88956.5311000.230.2340.0380.9991234.81332959.991
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.892.97971.6351.7850.7010.6370.96.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADFREE R-VALUE2.8956.531.351327765699.60.19210.18920.19070.24650.242Random
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.096
f_angle_d1.517
f_chiral_restr0.093
f_bond_d0.012
f_plane_restr0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3951
Nucleic Acid Atoms
Solvent Atoms5
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
xia2data reduction
AutoSolphasing
PDB_EXTRACTdata extraction