5K4T

Three-dimensional structure of L-threonine 3-dehydrogenase from Trypanosoma brucei refined to 2.1 angstroms


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1M MES, 0.2M ammonium sulphate, 30% PEG w/v 5000 MME
Crystal Properties
Matthews coefficientSolvent content
2.7555.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.759α = 90
b = 91.759β = 90
c = 93.598γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9173DiamondI04-1

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
12.129.07399.930.05433.612.622705

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.129.0722705122999.930.16370.1610.2163RANDOM29.747
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_4_deg20.346
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg7.296
r_mcangle_it3.912
r_mcbond_it2.619
r_mcbond_other2.619
r_angle_refined_deg2.004
r_angle_other_deg0.954
r_chiral_restr0.127
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.979
r_dihedral_angle_4_deg20.346
r_dihedral_angle_3_deg15.05
r_dihedral_angle_1_deg7.296
r_mcangle_it3.912
r_mcbond_it2.619
r_mcbond_other2.619
r_angle_refined_deg2.004
r_angle_other_deg0.954
r_chiral_restr0.127
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2511
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
xia2data scaling