6O64

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 2 (AtSPDS2)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292Morpheus screen G4 (Carboxylic acids, buffer system 1, precipitant mix 4)
Crystal Properties
Matthews coefficientSolvent content
2.3748.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.646α = 90
b = 162.699β = 100.21
c = 97.494γ = 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
124697.10.0560.99916.54.3125268-3
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)
122.0797.10.5570.8442.54.3

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 REPLACEMENTTHROUGHOUT242.54124006123480.160.176590.176050.23052RANDOM35.204
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]
-0.040.41-0.360.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.453
r_dihedral_angle_3_deg16.032
r_dihedral_angle_4_deg14.39
r_dihedral_angle_1_deg8.394
r_long_range_B_refined5.593
r_long_range_B_other5.552
r_scangle_other3.244
r_mcangle_it2.95
r_mcangle_other2.95
r_scbond_other1.996
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.453
r_dihedral_angle_3_deg16.032
r_dihedral_angle_4_deg14.39
r_dihedral_angle_1_deg8.394
r_long_range_B_refined5.593
r_long_range_B_other5.552
r_scangle_other3.244
r_mcangle_it2.95
r_mcangle_other2.95
r_scbond_other1.996
r_scbond_it1.995
r_angle_refined_deg1.855
r_mcbond_it1.798
r_mcbond_other1.798
r_angle_other_deg1.373
r_chiral_restr0.092
r_bond_refined_d0.014
r_gen_planes_refined0.011
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 Atoms17482
Nucleic Acid Atoms
Solvent Atoms936
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing