6O65

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1) in complex with decarboxylated S-adenosylmethionine and cyclohexylamine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52920.18 M ammonium sulfate, 0.09 M BIS-TRIS, 22% PEG 3350, cryoprotection 25% MPD
Crystal Properties
Matthews coefficientSolvent content
2.5551.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.201α = 90
b = 107.558β = 95.3
c = 142.424γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2019-02-15MSINGLE 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
11.847.693.40.0890.9978.23.3200872-3
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)
11.81.8595.50.4130.8332.73.5

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 REPLACEMENTTHROUGHOUT1.847.6201969162181.640.219050.218710.26095RANDOM18.225
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]
-0.510.19-0.20.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.702
r_dihedral_angle_3_deg14.999
r_dihedral_angle_4_deg14.047
r_dihedral_angle_1_deg7.982
r_long_range_B_refined5.321
r_long_range_B_other5.229
r_scangle_other2.057
r_angle_refined_deg1.975
r_mcangle_it1.736
r_mcangle_other1.736
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.702
r_dihedral_angle_3_deg14.999
r_dihedral_angle_4_deg14.047
r_dihedral_angle_1_deg7.982
r_long_range_B_refined5.321
r_long_range_B_other5.229
r_scangle_other2.057
r_angle_refined_deg1.975
r_mcangle_it1.736
r_mcangle_other1.736
r_angle_other_deg1.548
r_scbond_it1.364
r_scbond_other1.35
r_mcbond_it1.135
r_mcbond_other1.135
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.013
r_bond_other_d0.009
r_gen_planes_other0.006
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 Atoms17981
Nucleic Acid Atoms
Solvent Atoms2103
Heterogen Atoms290

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction