5Y1E

monomeric L-threonine 3-dehydrogenase from metagenome database (L-Ser and NAD+ bound form)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3WMX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP27720% (w/v) PEG 3350, 0.2M Sodium fluoride
Crystal Properties
Matthews coefficientSolvent content
2.0339.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.594α = 90
b = 50.857β = 105.6
c = 55.252γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2016-06-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.10Photon FactoryBL-1A

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
11.954.298.717.26.623337
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.95

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 REPLACEMENTTHROUGHOUT3WMX1.954.2222187115098.030.160220.158220.199RANDOM19.277
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
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.024
r_dihedral_angle_4_deg16.069
r_dihedral_angle_3_deg15.26
r_dihedral_angle_1_deg7.209
r_long_range_B_other6.854
r_long_range_B_refined6.849
r_scangle_other5.928
r_scbond_it4.049
r_scbond_other4.014
r_mcangle_it3.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.024
r_dihedral_angle_4_deg16.069
r_dihedral_angle_3_deg15.26
r_dihedral_angle_1_deg7.209
r_long_range_B_other6.854
r_long_range_B_refined6.849
r_scangle_other5.928
r_scbond_it4.049
r_scbond_other4.014
r_mcangle_it3.09
r_mcangle_other3.089
r_mcbond_it2.308
r_mcbond_other2.292
r_angle_refined_deg1.489
r_angle_other_deg0.811
r_chiral_restr0.211
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms2479
Nucleic Acid Atoms
Solvent Atoms156
Heterogen Atoms51

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing