5LC1

L-threonine dehydrogenase from Trypanosoma brucei with NAD and the inhibitor pyruvate bound.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5L9A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES pH 7.5, 20 % w/v PEG 10K; TDH 2.0 mg/ml, 1 mM NAD(+), 30 mM pyruvate.
Crystal Properties
Matthews coefficientSolvent content
2.245.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.04α = 90
b = 276.49β = 90
c = 55.74γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.074ESRFID29

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
12.195.597.30.14511.47.511720421.2
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)
12.12.281.90.5253.23.3

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 REPLACEMENTTHROUGHOUT5L9A2.195.5111527556397.330.149520.146540.20763RANDOM22.767
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]
0.010.76-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.188
r_dihedral_angle_4_deg18.605
r_dihedral_angle_3_deg15.461
r_long_range_B_refined7.489
r_long_range_B_other7.124
r_dihedral_angle_1_deg6.874
r_scangle_other4.601
r_scbond_it2.986
r_scbond_other2.986
r_mcangle_other2.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.188
r_dihedral_angle_4_deg18.605
r_dihedral_angle_3_deg15.461
r_long_range_B_refined7.489
r_long_range_B_other7.124
r_dihedral_angle_1_deg6.874
r_scangle_other4.601
r_scbond_it2.986
r_scbond_other2.986
r_mcangle_other2.675
r_mcangle_it2.674
r_angle_refined_deg1.794
r_mcbond_it1.753
r_mcbond_other1.752
r_angle_other_deg1.035
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15010
Nucleic Acid Atoms
Solvent Atoms1962
Heterogen Atoms326

Software

Software
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
REFMACrefinement