5TR3

2.5 Angstrom Resolution Crystal Structure of Dihydrolipoyl Dehydrogenase from Pseudomonas putida in Complex with FAD.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Protein: 13.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 1mM FAD; Screen: Classics II(F10), 0.2M Sodim chloride, 0.01M Tris HCl (pH 6.5), 25% (w/v) PEG 3350.
Crystal Properties
Matthews coefficientSolvent content
2.7555.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.886α = 90
b = 132.113β = 90
c = 158.132γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2016-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.53099.90.0750.07520.14.942116-351.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.541000.6320.8372.64.9

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 REPLACEMENTTHROUGHOUT3LAD2.529.4240007204499.770.227290.22540.26422RANDOM60.399
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]
-1.477.17-5.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg14.204
r_dihedral_angle_3_deg10.771
r_long_range_B_refined5.665
r_long_range_B_other5.651
r_scangle_other2.822
r_mcangle_other2.763
r_mcangle_it2.763
r_dihedral_angle_1_deg1.998
r_scbond_it1.758
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.201
r_dihedral_angle_4_deg14.204
r_dihedral_angle_3_deg10.771
r_long_range_B_refined5.665
r_long_range_B_other5.651
r_scangle_other2.822
r_mcangle_other2.763
r_mcangle_it2.763
r_dihedral_angle_1_deg1.998
r_scbond_it1.758
r_scbond_other1.754
r_mcbond_it1.733
r_mcbond_other1.732
r_angle_refined_deg1.459
r_angle_other_deg0.877
r_chiral_restr0.081
r_gen_planes_refined0.023
r_gen_planes_other0.02
r_bond_refined_d0.009
r_bond_other_d0.001
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6924
Nucleic Acid Atoms
Solvent Atoms251
Heterogen Atoms120

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing