5HN4

Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus kodakarensis complexed with Mn and homoisocitrate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HN3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52932-propanol, HEPES, sodium chloride
Crystal Properties
Matthews coefficientSolvent content
5.9979.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 113.669α = 90
b = 113.669β = 90
c = 143.226γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702014-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.0Photon FactoryAR-NE3A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.64143.2399.20.08541.87.728294
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.642.691000.5943.97.8

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 REPLACEMENTTHROUGHOUT5HN32.64143.2326653134299.090.202060.201130.22033RANDOM66.852
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]
0.020.02-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.963
r_dihedral_angle_4_deg20.103
r_dihedral_angle_3_deg17.849
r_long_range_B_other9.555
r_long_range_B_refined9.554
r_scangle_other7.729
r_mcangle_other6.28
r_mcangle_it6.276
r_dihedral_angle_1_deg6.164
r_scbond_it5.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.963
r_dihedral_angle_4_deg20.103
r_dihedral_angle_3_deg17.849
r_long_range_B_other9.555
r_long_range_B_refined9.554
r_scangle_other7.729
r_mcangle_other6.28
r_mcangle_it6.276
r_dihedral_angle_1_deg6.164
r_scbond_it5.147
r_scbond_other5.145
r_mcbond_it4.432
r_mcbond_other4.414
r_angle_refined_deg1.555
r_angle_other_deg0.899
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms2505
Nucleic Acid Atoms
Solvent Atoms15
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction