6J27

Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Q3M 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Reservoir: 0.04 M sodium chloride , 0.04 M Tris pH 8.0, 27%(v/v) PEG 350MME
Crystal Properties
Matthews coefficientSolvent content
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.57α = 90
b = 158.606β = 118.95
c = 71.936γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2016-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL32XU1.10000SPring-8BL32XU

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
11.665099.315.15.3156847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.661.71

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 REPLACEMENTTHROUGHOUT2Q3M1.6650148976782298.540.169180.167240.20618RANDOM28.17
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]
-1.21-0.443.28-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.32
r_dihedral_angle_4_deg21.425
r_dihedral_angle_3_deg15.133
r_long_range_B_refined6.455
r_long_range_B_other6.436
r_dihedral_angle_1_deg5.782
r_scangle_other5.219
r_scbond_it3.422
r_scbond_other3.421
r_mcangle_it2.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.32
r_dihedral_angle_4_deg21.425
r_dihedral_angle_3_deg15.133
r_long_range_B_refined6.455
r_long_range_B_other6.436
r_dihedral_angle_1_deg5.782
r_scangle_other5.219
r_scbond_it3.422
r_scbond_other3.421
r_mcangle_it2.942
r_mcangle_other2.942
r_mcbond_it2.165
r_mcbond_other2.165
r_angle_refined_deg1.92
r_angle_other_deg1.099
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms10885
Nucleic Acid Atoms
Solvent Atoms688
Heterogen Atoms231

Software

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