6U01

Dihydrodipicolinate synthase (DHDPS) from C.jejuni, N84D mutant with pyruvate bound in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4LY8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH7.4288.150.7 M Magnesium acetate, 10 % PEG8000 0.1 M Sodium acetate (pH 7.4)
Crystal Properties
Matthews coefficientSolvent content
2.4149.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.99α = 90
b = 231.42β = 90
c = 200.65γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-05-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.9795CLSI08B1-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.8743.43699.20.0940.1120.9927.853.43716126928.12
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.871.9299.90.5670.670.7422.063.505

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4LY81.8743.4361.35161254806499.160.1910.18940.221328.3492
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_d14.823
f_angle_d0.798
f_chiral_restr0.049
f_plane_restr0.005
f_bond_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13672
Nucleic Acid Atoms
Solvent Atoms987
Heterogen Atoms140

Software

Software
Software NamePurpose
PHENIXrefinement
Cootmodel building
XSCALEdata scaling
HKL-3000data collection
PHENIXphasing