6J28 | pdb_00006j28

Crystal structure of the branched-chain polyamine synthase C9 mutein from Thermus thermophilus (Tth-BpsA C9) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5293Reservoir 0.02 M sodium chloride, 0.05 M MES pH 5.5, 14%(v/v) PEG 350MME
Crystal Properties
Matthews coefficientSolvent content
2.0941.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.777α = 90
b = 158.518β = 118.94
c = 72.018γ = 90
Symmetry
Space GroupP 1 21 1

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
11.95099.219.66.7106347
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.97

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.949.33101022528599.610.202540.199870.210.254090.26RANDOM24.109
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.211
r_dihedral_angle_4_deg18.593
r_dihedral_angle_3_deg15.165
r_dihedral_angle_1_deg6.624
r_long_range_B_refined5.415
r_long_range_B_other5.415
r_scangle_other3.845
r_mcangle_it2.686
r_mcangle_other2.686
r_scbond_other2.448
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10912
Nucleic Acid Atoms
Solvent Atoms499
Heterogen Atoms174

Software

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