6J26

Crystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293Reservoir: 0.015 M tricine pH 8.5, 24%(v/v) PEG 4000
Crystal Properties
Matthews coefficientSolvent content
1.9837.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.17α = 90
b = 74.17β = 90
c = 105.934γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
125010026.110.144104
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.07

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 REPLACEMENTTHROUGHOUT5XNC240.8741889218299.910.197530.196030.22769RANDOM32.088
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]
0.010.010.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.659
r_dihedral_angle_3_deg12.51
r_dihedral_angle_4_deg12.32
r_dihedral_angle_1_deg5.626
r_long_range_B_refined2.162
r_long_range_B_other2.077
r_angle_refined_deg1.136
r_scangle_other0.999
r_mcangle_it0.942
r_mcangle_other0.941
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.659
r_dihedral_angle_3_deg12.51
r_dihedral_angle_4_deg12.32
r_dihedral_angle_1_deg5.626
r_long_range_B_refined2.162
r_long_range_B_other2.077
r_angle_refined_deg1.136
r_scangle_other0.999
r_mcangle_it0.942
r_mcangle_other0.941
r_angle_other_deg0.873
r_scbond_it0.572
r_scbond_other0.572
r_mcbond_it0.536
r_mcbond_other0.536
r_chiral_restr0.056
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
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 Atoms5712
Nucleic Acid Atoms
Solvent Atoms204
Heterogen Atoms77

Software

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