6O63

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52920.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% PEG 3350, cryoprotection 25% glycerol
Crystal Properties
Matthews coefficientSolvent content
2.0239.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.536α = 90
b = 76.338β = 104.68
c = 90.192γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2018-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.00APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.844.695.40.0550.99914.14.195958-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8678.50.5470.7872.54

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.843.4694875108387.890.165830.165240.22209RANDOM24.503
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]
-0.21-0.160.5-0.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.273
r_dihedral_angle_3_deg14.21
r_dihedral_angle_4_deg9.671
r_dihedral_angle_1_deg7.817
r_long_range_B_refined5.98
r_long_range_B_other5.979
r_scangle_other2.274
r_mcangle_it1.855
r_mcangle_other1.855
r_angle_refined_deg1.796
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.273
r_dihedral_angle_3_deg14.21
r_dihedral_angle_4_deg9.671
r_dihedral_angle_1_deg7.817
r_long_range_B_refined5.98
r_long_range_B_other5.979
r_scangle_other2.274
r_mcangle_it1.855
r_mcangle_other1.855
r_angle_refined_deg1.796
r_angle_other_deg1.463
r_scbond_it1.448
r_scbond_other1.424
r_mcbond_it1.142
r_mcbond_other1.142
r_chiral_restr0.095
r_bond_refined_d0.013
r_gen_planes_refined0.011
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 Atoms8798
Nucleic Acid Atoms
Solvent Atoms986
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction