3FMX

Crystal structure of Tartrate dehydrogenase from Pseudomonas putida complexed with NADH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52931.65 M ammonium sulfate, 0.2 M ammonium tartrate, 0.01 M DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
469.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 182.906α = 90
b = 182.906β = 90
c = 66.98γ = 120
Symmetry
Space GroupP 6 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2008-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.03APS22-BM

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
12.85084.714251
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.980.53.3

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 REPLACEMENTTHROUGHOUT3FLK2.955011632604850.261910.260170.29684RANDOM55.794
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]
-0.13-0.06-0.130.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.201
r_dihedral_angle_3_deg21.116
r_dihedral_angle_4_deg17.004
r_dihedral_angle_1_deg6.561
r_angle_refined_deg1.383
r_nbtor_refined0.321
r_symmetry_vdw_refined0.245
r_nbd_refined0.243
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.201
r_dihedral_angle_3_deg21.116
r_dihedral_angle_4_deg17.004
r_dihedral_angle_1_deg6.561
r_angle_refined_deg1.383
r_nbtor_refined0.321
r_symmetry_vdw_refined0.245
r_nbd_refined0.243
r_xyhbond_nbd_refined0.2
r_symmetry_hbond_refined0.145
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2813
Nucleic Acid Atoms
Solvent Atoms17
Heterogen Atoms45

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling