4M19

dihydrodipicolinate synthase from C. jejuni with pyruvate bound to the active site and Lysine bound to allosteric site


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1hanging drop8.528835% PEG3350, 0.3 M NH4SO4, 0.1 mM TRIS, pH 8.5, hanging drop, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.64α = 90
b = 96.99β = 111.53
c = 79.56γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDRAYONIX MX300HE2012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08B1-10.9796CLSI08B1-1

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
11.715078.70.08213.82937139371321.24
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)
11.711.8233.90.0120.86

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 REPLACEMENT4LY8248.49527335173351366897.720.16710.16710.1650.2043random24.095
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]
6.86093.4359-1.8996-4.9613
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.246
f_angle_d1.032
f_chiral_restr0.089
f_bond_d0.006
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9089
Nucleic Acid Atoms
Solvent Atoms523
Heterogen Atoms68

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACTdata extraction