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Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 292 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% PEG 3350, cryoprotection 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.536 α = 90 b = 76.338 β = 104.68 c = 90.192 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300-HS 2018-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.00 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 44.6 95.4 0.055 0.999 14.1 4.1 95958 -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) Redundancy Number Unique Reflections (All) 1 1.8 1.86 78.5 0.547 0.787 2.5 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 43.46 94875 1083 87.89 0.16583 0.16524 0.1744 0.22209 0.2302 RANDOM 24.503
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 -0.16 0.5 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.273 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_4_deg 9.671 r_dihedral_angle_1_deg 7.817 r_long_range_B_refined 5.98 r_long_range_B_other 5.979 r_scangle_other 2.274 r_mcangle_it 1.855 r_mcangle_other 1.855 r_angle_refined_deg 1.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.273 r_dihedral_angle_3_deg 14.21 r_dihedral_angle_4_deg 9.671 r_dihedral_angle_1_deg 7.817 r_long_range_B_refined 5.98 r_long_range_B_other 5.979 r_scangle_other 2.274 r_mcangle_it 1.855 r_mcangle_other 1.855 r_angle_refined_deg 1.796 r_angle_other_deg 1.463 r_scbond_it 1.448 r_scbond_other 1.424 r_mcbond_it 1.142 r_mcbond_other 1.142 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 8798 Nucleic Acid Atoms Solvent Atoms 986 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement PHASER phasing STARANISO data scaling XDS data reduction