5Y1F

Monomeric L-threonine 3-dehydrogenase from metagenome database (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
2.0238.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.494α = 90
b = 48.927β = 104.71
c = 56.364γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702016-05-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.00Photon FactoryAR-NE3A

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
11.2554.991.528.96.375876
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.251.28

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 REPLACEMENTTHROUGHOUT3WMX1.2554.8972123374391.330.158270.157090.18055RANDOM14.098
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.026
r_dihedral_angle_4_deg17.639
r_dihedral_angle_3_deg14.959
r_dihedral_angle_1_deg6.78
r_long_range_B_refined6.585
r_long_range_B_other6.249
r_scangle_other4.605
r_scbond_it3.204
r_scbond_other3.203
r_mcangle_other1.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.026
r_dihedral_angle_4_deg17.639
r_dihedral_angle_3_deg14.959
r_dihedral_angle_1_deg6.78
r_long_range_B_refined6.585
r_long_range_B_other6.249
r_scangle_other4.605
r_scbond_it3.204
r_scbond_other3.203
r_mcangle_other1.893
r_mcangle_it1.892
r_angle_refined_deg1.652
r_mcbond_it1.359
r_mcbond_other1.349
r_angle_other_deg0.802
r_chiral_restr0.271
r_gen_planes_refined0.015
r_bond_refined_d0.014
r_gen_planes_other0.003
r_bond_other_d0.001
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 Atoms2499
Nucleic Acid Atoms
Solvent Atoms426
Heterogen Atoms44

Software

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