2GN0

Crystal structure of dimeric biodegradative threonine deaminase (TdcB) from Salmonella typhimurium at 1.7 A resolution (Triclinic form with one complete subunit built in alternate conformation)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62980.1 M citrate buffer pH 6.0, 20% PEG 3350 and 15% t-butanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0640.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.675α = 66.12
b = 76.827β = 89.16
c = 78.501γ = 77.08
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plateOsmic mirror2005-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.542

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
11.73093.10.04126.5815.6412868012868026
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)
11.71.7686.90.4262.7611167

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 REPLACEMENTTHROUGHOUTBiosynthetic threonine deaminase (1TDJ)1.720113742599892.920.19010.188420.22154RANDOM22.819
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]
0.80.330.31-0.640.01-0.32
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.148
r_dihedral_angle_4_deg11.526
r_dihedral_angle_3_deg11.49
r_dihedral_angle_1_deg5.106
r_scangle_it1.979
r_scbond_it1.187
r_angle_refined_deg1.031
r_angle_other_deg0.712
r_mcangle_it0.666
r_mcbond_it0.367
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.148
r_dihedral_angle_4_deg11.526
r_dihedral_angle_3_deg11.49
r_dihedral_angle_1_deg5.106
r_scangle_it1.979
r_scbond_it1.187
r_angle_refined_deg1.031
r_angle_other_deg0.712
r_mcangle_it0.666
r_mcbond_it0.367
r_nbd_refined0.195
r_symmetry_vdw_other0.19
r_symmetry_vdw_refined0.181
r_nbtor_refined0.166
r_nbd_other0.16
r_symmetry_hbond_refined0.14
r_xyhbond_nbd_refined0.117
r_symmetry_metal_ion_refined0.103
r_mcbond_other0.092
r_nbtor_other0.079
r_metal_ion_refined0.078
r_chiral_restr0.057
r_symmetry_hbond_other0.034
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9636
Nucleic Acid Atoms
Solvent Atoms780
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing