5Z21

The ternary structure of D-lactate dehydrogenase from Fusobacterium nucleatum with NADH and oxamate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J49 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52982 mM NADH, 25 mM oxamate, 100 mM acetate buffer pH 5, 4% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5852.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.23α = 90
b = 159.74β = 90
c = 90γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102013-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A0.97911Photon FactoryAR-NW12A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
12.342.011000.1250.050.99613.57.275787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.421000.640.2540.7383.27.3

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 REPLACEMENTTHROUGHOUT1J492.342.0171921381099.970.226790.225460.25142RANDOM33.925
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.99
r_dihedral_angle_4_deg24.522
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg6.21
r_long_range_B_refined3.963
r_long_range_B_other3.96
r_scangle_other2.668
r_mcangle_it2.405
r_mcangle_other2.405
r_scbond_it1.638
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.99
r_dihedral_angle_4_deg24.522
r_dihedral_angle_3_deg16.069
r_dihedral_angle_1_deg6.21
r_long_range_B_refined3.963
r_long_range_B_other3.96
r_scangle_other2.668
r_mcangle_it2.405
r_mcangle_other2.405
r_scbond_it1.638
r_scbond_other1.638
r_angle_refined_deg1.629
r_mcbond_it1.541
r_mcbond_other1.541
r_angle_other_deg1.332
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.008
r_gen_planes_other0.007
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 Atoms10490
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms200

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALAdata scaling
BUCCANEERmodel building