2EJV

Crystal structure of threonine 3-dehydrogenase complexed with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DQ4PDB ENTRY 2DQ4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.8M Sodium Acetate, 0.1M Mes pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.8774.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.758α = 90
b = 135.758β = 90
c = 268.593γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS V2003-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1.0SPring-8BL45XU

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
12.555099.54851055.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2DQ42.5519.9948074484999.50.2070.2070.236RANDOM49.6
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]
2.394.442.39-4.77
RMS Deviations
KeyRefinement Restraint Deviation
c_scbond_it30.95
c_scangle_it28.18
c_dihedral_angle_d24.3
c_mcangle_it1.75
c_angle_deg1.5
c_mcbond_it1.08
c_improper_angle_d0.92
c_bond_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5129
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms92

Software

Software
Software NamePurpose
CNSrefinement
CrystalCleardata collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing