2O0T

The three dimensional structure of diaminopimelate decarboxylase from Mycobacterium tuberculosis reveals a tetrameric enzyme organisation


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
129120-23%(w/v) polyethylene glycol monomethylether 5000, 0.1 M MES, 60 mM ammonium sulfate, pH 6.1-6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.78α = 90
b = 106.88β = 104.99
c = 121.93γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2004-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HamburgX11

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
12.339999.90.07717.848020342.5
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)
12.332.3799.90.6232.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HKV2.333078557159799.90.1920.1910.241RANDOM46.01
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]
1.54-1.52-1.69-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.421
r_dihedral_angle_4_deg20.851
r_dihedral_angle_3_deg18.379
r_dihedral_angle_1_deg6.481
r_scangle_it5.851
r_scbond_it4.166
r_angle_refined_deg1.788
r_mcangle_it1.643
r_mcbond_it0.924
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.421
r_dihedral_angle_4_deg20.851
r_dihedral_angle_3_deg18.379
r_dihedral_angle_1_deg6.481
r_scangle_it5.851
r_scbond_it4.166
r_angle_refined_deg1.788
r_mcangle_it1.643
r_mcbond_it0.924
r_nbtor_refined0.306
r_symmetry_vdw_refined0.289
r_symmetry_hbond_refined0.242
r_nbd_refined0.215
r_xyhbond_nbd_refined0.152
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13350
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing