5L9A

L-threonine dehydrogenase from trypanosoma brucei.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YY7 

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
Crystal Properties
Matthews coefficientSolvent content
2.244.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.985α = 72.46
b = 57.722β = 70.38
c = 70.074γ = 73.2
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
11.4553.82950.08910.43.810905411.9
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)
11.451.5382.10.3982.72.3

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 REPLACEMENTTHROUGHOUT2yy71.4546.82103550549195.030.102540.099690.15643RANDOM16.591
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]
-0.04-0.030.010.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.177
r_dihedral_angle_2_deg35.633
r_dihedral_angle_4_deg14.77
r_dihedral_angle_3_deg13.769
r_sphericity_bonded11.902
r_dihedral_angle_1_deg6.466
r_long_range_B_refined5.313
r_rigid_bond_restr4.414
r_long_range_B_other4.115
r_scangle_other3.8
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free40.177
r_dihedral_angle_2_deg35.633
r_dihedral_angle_4_deg14.77
r_dihedral_angle_3_deg13.769
r_sphericity_bonded11.902
r_dihedral_angle_1_deg6.466
r_long_range_B_refined5.313
r_rigid_bond_restr4.414
r_long_range_B_other4.115
r_scangle_other3.8
r_scbond_it3.286
r_scbond_other3.286
r_angle_refined_deg2.07
r_mcangle_it1.837
r_mcangle_other1.837
r_mcbond_it1.525
r_mcbond_other1.491
r_angle_other_deg1.325
r_chiral_restr0.138
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.005
r_gen_planes_other0.003
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5011
Nucleic Acid Atoms
Solvent Atoms1335
Heterogen Atoms8

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement