3FSX

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298190 mM magnesium acetate tetrahydrate, 100 mM sodium cacodylate pH 6.5, 10 %(w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4850.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 216.99α = 90
b = 216.99β = 90
c = 216.99γ = 90
Symmetry
Space GroupI 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-06-13MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.0000MAX III911-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.1537.2110010.49174191416-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.1999.78.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.15309053690238112699.670.168560.167930.21945RANDOM30.215
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
r_dihedral_angle_2_deg28.299
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg14.173
r_scangle_it6.976
r_dihedral_angle_1_deg6.417
r_scbond_it4.645
r_mcangle_it1.966
r_angle_refined_deg1.724
r_mcbond_it1.075
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.299
r_dihedral_angle_4_deg19.042
r_dihedral_angle_3_deg14.173
r_scangle_it6.976
r_dihedral_angle_1_deg6.417
r_scbond_it4.645
r_mcangle_it1.966
r_angle_refined_deg1.724
r_mcbond_it1.075
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10866
Nucleic Acid Atoms
Solvent Atoms570
Heterogen Atoms53

Software

Software
Software NamePurpose
MxCuBEdata collection
Auto-Rickshawphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling